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From: Warren D. <wa...@de...> - 2005-11-18 01:26:45
|
A quick fix is to use the "retain_order" setting. set retain_order which will force PyMOL to honor the order of ATOMs in the PDB file over = the numeric ordering of residue identifiers. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Joel Tyndall > Sent: Thursday, November 17, 2005 12:15 PM > To: Anne M=F8lgaard; pym...@li... > Subject: Re: [PyMOL] displaying protein with propeptide >=20 > Hi Ann, >=20 > I would change the chain id of the propeptide in a text=20 > editor, to say P and remove the P from after the residue numbers. >=20 > J >=20 > Anne M=F8lgaard wrote: >=20 > >Hi, > > > >I am having problems displaying proteins with unusual residue=20 > >numbering, such as proteins with propeptides. An example is=20 > 1cs8, which=20 > >starts off like > >this: > > > >ATOM 1 N SER A 1P -32.762 23.978 22.929 0.00 34.26 > >N =20 > >ATOM 2 CA SER A 1P -32.360 24.645 21.660 0.00 34.08 > >C =20 > >ATOM 3 C SER A 1P -32.303 26.162 21.821 0.00 33.91 > >C =20 > >ATOM 4 O SER A 1P -32.838 26.712 22.786 0.00 33.82 > >O =20 > >ATOM 5 CB SER A 1P -33.338 24.274 20.541 0.00 34.28 > >C =20 > >ATOM 6 OG SER A 1P -34.684 24.406 20.971 0.00 34.36 > >O > >. > >. > >. > >And later on comes the sequence corresponding to the mature protein: > > > >ATOM 1060 N ALA A 1 11.470 66.852 16.148 1.00 22.69 > >N =20 > >ATOM 1061 CA ALA A 1 11.282 65.561 15.491 1.00 20.80 > >C =20 > >ATOM 1062 C ALA A 1 10.621 65.677 14.113 1.00 20.33 > >C =20 > >ATOM 1063 O ALA A 1 9.920 66.649 13.835 1.00 18.43 > >O =20 > >ATOM 1064 CB ALA A 1 10.451 64.636 16.393 1.00 19.50 > >C > >Etc.=20 > > > >If I open 1cs8 with PyMol, I can see everything in the "lines",=20 > >"sticks" and "surface" representation, but in ribbon or cartoon mode=20 > >only part of the protein is shown. What do I have to do to=20 > show the whole sequence? > > > >How do I select residues with a "P" appended to the residue=20 > number? If=20 > >I say "select resi 1P-5P" I get both 1P-5P and 1-5. > > > >Any help will be appreciated! (I am using PyMol version 0.98=20 > for Windows). > > > >- Anne > > > >-------------------------------------------- > >Anne M=F8lgaard, Ph.D. > >Center for Biological Sequence Analysis BioCentrum-DTU, Building 208=20 > >DK-2800 Lyngby > > > >Email: an...@cb... > >Phone: (+45)4525 2472 > >-------------------------------------------- > > > > > > > > > >------------------------------------------------------- > >This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > >Register for a JBoss Training Course. Free Certification Exam > >for All Training Attendees Through End of 2005. For more info visit: > >http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick > >_______________________________________________ > >PyMOL-users mailing list > >PyM...@li... > >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > =20 > > >=20 > --=20 > Joel Tyndall, PhD >=20 > Lecturer > National School of Pharmacy > University of Otago > PO Box 913 Dunedin > New Zealand =20 >=20 > Pukenga > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 913 Otepoti > Aotearoa >=20 > Ph / Waea +64 3 4797293=20 > Fax / Waeawhakaahua +64 3 4797034 >=20 >=20 >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
|
From: Warren D. <wa...@de...> - 2005-11-18 01:41:57
|
I'm not sure how version-dependent this is, but setting connect_mode to = 1 before loading the PDB should disable distance-based connectivity = determination. set connect_mode, 1 load CONECT_only_pdb.pdb -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Eric Zollars > Sent: Thursday, November 17, 2005 5:36 PM > To: pym...@li... > Subject: Re: [PyMOL] displaying protein with propeptide >=20 > Is there a similar command to force PyMOL to use only CONECT=20 > lines in the pdb file instead of generating connectivity by distance? >=20 > Eric >=20 > Warren DeLano wrote: > > A quick fix is to use the "retain_order" setting. > >=20 > > set retain_order > >=20 > > which will force PyMOL to honor the order of ATOMs in the=20 > PDB file over the numeric ordering of residue identifiers. > >=20 > > Cheers, > > Warren > >=20 > > -- > > Warren L. DeLano, Ph.D. =20 > > Principal Scientist > >=20 > > . DeLano Scientific LLC =20 > > . 400 Oyster Point Blvd., Suite 213 =20 > > . South San Francisco, CA 94080 USA =20 > > . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 > > . Fax:(650)-872-0273 Cell:(650)-346-1154 > > . mailto:wa...@de... =20 > > =20 > >=20 > >=20 > >>-----Original Message----- > >>From: pym...@li... > >>[mailto:pym...@li...] On Behalf Of Joel=20 > >>Tyndall > >>Sent: Thursday, November 17, 2005 12:15 PM > >>To: Anne M=F8lgaard; pym...@li... > >>Subject: Re: [PyMOL] displaying protein with propeptide > >> > >>Hi Ann, > >> > >>I would change the chain id of the propeptide in a text=20 > editor, to say=20 > >>P and remove the P from after the residue numbers. > >> > >>J > >> > >>Anne M=F8lgaard wrote: > >> > >> > >>>Hi, > >>> > >>>I am having problems displaying proteins with unusual residue=20 > >>>numbering, such as proteins with propeptides. An example is > >> > >>1cs8, which > >> > >>>starts off like > >>>this: > >>> > >>>ATOM 1 N SER A 1P -32.762 23.978 22.929 0.00 34.26 > >>>N =20 > >>>ATOM 2 CA SER A 1P -32.360 24.645 21.660 0.00 34.08 > >>>C =20 > >>>ATOM 3 C SER A 1P -32.303 26.162 21.821 0.00 33.91 > >>>C =20 > >>>ATOM 4 O SER A 1P -32.838 26.712 22.786 0.00 33.82 > >>>O =20 > >>>ATOM 5 CB SER A 1P -33.338 24.274 20.541 0.00 34.28 > >>>C =20 > >>>ATOM 6 OG SER A 1P -34.684 24.406 20.971 0.00 34.36 > >>>O > >>>. > >>>. > >>>. > >>>And later on comes the sequence corresponding to the=20 > mature protein: > >>> > >>>ATOM 1060 N ALA A 1 11.470 66.852 16.148 1.00 22.69 > >>>N =20 > >>>ATOM 1061 CA ALA A 1 11.282 65.561 15.491 1.00 20.80 > >>>C =20 > >>>ATOM 1062 C ALA A 1 10.621 65.677 14.113 1.00 20.33 > >>>C =20 > >>>ATOM 1063 O ALA A 1 9.920 66.649 13.835 1.00 18.43 > >>>O =20 > >>>ATOM 1064 CB ALA A 1 10.451 64.636 16.393 1.00 19.50 > >>>C > >>>Etc.=20 > >>> > >>>If I open 1cs8 with PyMol, I can see everything in the "lines",=20 > >>>"sticks" and "surface" representation, but in ribbon or=20 > cartoon mode=20 > >>>only part of the protein is shown. What do I have to do to > >> > >>show the whole sequence? > >> > >>>How do I select residues with a "P" appended to the residue > >> > >>number? If > >> > >>>I say "select resi 1P-5P" I get both 1P-5P and 1-5. > >>> > >>>Any help will be appreciated! (I am using PyMol version 0.98 > >> > >>for Windows). > >> > >>>- Anne > >>> > >>>-------------------------------------------- > >>>Anne M=F8lgaard, Ph.D. > >>>Center for Biological Sequence Analysis BioCentrum-DTU,=20 > Building 208=20 > >>>DK-2800 Lyngby > >>> > >>>Email: an...@cb... > >>>Phone: (+45)4525 2472 > >>>-------------------------------------------- > >>> > >>> > >>> > >>> > >>>------------------------------------------------------- > >>>This SF.Net email is sponsored by the JBoss Inc. Get=20 > Certified Today=20 > >>>Register for a JBoss Training Course. Free Certification Exam for=20 > >>>All Training Attendees Through End of 2005. For more info visit: > >>>http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick > >>>_______________________________________________ > >>>PyMOL-users mailing list > >>>PyM...@li... > >>>https://lists.sourceforge.net/lists/listinfo/pymol-users > >>> > >>>=20 > >>> > >> > >>-- > >>Joel Tyndall, PhD > >> > >>Lecturer > >>National School of Pharmacy > >>University of Otago > >>PO Box 913 Dunedin > >>New Zealand =20 > >> > >>Pukenga > >>Te Kura Taiwhanga Putaiao > >>Te Whare Wananga o Otago > >>Pouaka Poutapeta 913 Otepoti > >>Aotearoa > >> > >>Ph / Waea +64 3 4797293=20 > >>Fax / Waeawhakaahua +64 3 4797034 > >> > >> > >> > >> > >> > >>------------------------------------------------------- > >>This SF.Net email is sponsored by the JBoss Inc. Get=20 > Certified Today=20 > >>Register for a JBoss Training Course. Free Certification=20 > Exam for All=20 > >>Training Attendees Through End of 2005. For more info visit: > >>http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick > >>_______________________________________________ > >>PyMOL-users mailing list > >>PyM...@li... > >>https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > >> > >> > >> > >=20 > >=20 > >=20 > > ------------------------------------------------------- > > This SF.Net email is sponsored by the JBoss Inc. Get=20 > Certified Today=20 > > Register for a JBoss Training Course. Free Certification=20 > Exam for All=20 > > Training Attendees Through End of 2005. For more info visit: > > http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get=20 > Certified Today Register for a JBoss Training Course. Free=20 > Certification Exam for All Training Attendees Through End of=20 > 2005. For more info visit: > http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
|
From: Michael G. L. <ml...@um...> - 2005-11-18 22:00:52
|
This is awesome. It looks like this has been a valid setting for a *long*=
=20
time, but I've never seen it. I look at a lot of MCSS-type structures,=20
and I have some really painful scripts that get the bonds right once the=20
structure is loaded in PyMOL. Now, I can just stamp the CONECT records at=
=20
the end of the file and load things up in connect_mode=3D1 world and=20
everything works. Speaking of which, I made a little bash shell script to=
=20
launch PyMOL this way:
pymol -d "cmd.set('connect_mode',1)" $@
It took me a couple of tries to get that right. The documentation for=20
command-line options says
-d <string> Run pymol command string upon startup.
so I first tried
pymol -d "set connect_mode,1" $@
but that doesn't work. Is this a documentation typo? I thought a PyMOL=20
command string was anything you could type at the PyMOL command prompt.
-michael
--
www.umich.edu/~mlerner | _ |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan
it's a cheer-ocracy. | - against HTML email X | Biophysics
-Torrence, Bring It On| / \ | mlerner@umich
On Thu, 17 Nov 2005, Warren DeLano wrote:
> I'm not sure how version-dependent this is, but setting connect_mode to 1=
before loading the PDB should disable distance-based connectivity determin=
ation.
>
> set connect_mode, 1
>
> load CONECT_only_pdb.pdb
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of
>> Eric Zollars
>> Sent: Thursday, November 17, 2005 5:36 PM
>> To: pym...@li...
>> Subject: Re: [PyMOL] displaying protein with propeptide
>>
>> Is there a similar command to force PyMOL to use only CONECT
>> lines in the pdb file instead of generating connectivity by distance?
>>
>> Eric
>>
>> Warren DeLano wrote:
>>> A quick fix is to use the "retain_order" setting.
>>>
>>> set retain_order
>>>
>>> which will force PyMOL to honor the order of ATOMs in the
>> PDB file over the numeric ordering of residue identifiers.
>>>
>>> Cheers,
>>> Warren
>>>
>>> --
>>> Warren L. DeLano, Ph.D.
>>> Principal Scientist
>>>
>>> . DeLano Scientific LLC
>>> . 400 Oyster Point Blvd., Suite 213
>>> . South San Francisco, CA 94080 USA
>>> . Biz:(650)-872-0942 Tech:(650)-872-0834
>>> . Fax:(650)-872-0273 Cell:(650)-346-1154
>>> . mailto:wa...@de...
>>>
>>>
>>>
>>>> -----Original Message-----
>>>> From: pym...@li...
>>>> [mailto:pym...@li...] On Behalf Of Joel
>>>> Tyndall
>>>> Sent: Thursday, November 17, 2005 12:15 PM
>>>> To: Anne M=F8lgaard; pym...@li...
>>>> Subject: Re: [PyMOL] displaying protein with propeptide
>>>>
>>>> Hi Ann,
>>>>
>>>> I would change the chain id of the propeptide in a text
>> editor, to say
>>>> P and remove the P from after the residue numbers.
>>>>
>>>> J
>>>>
>>>> Anne M=F8lgaard wrote:
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> I am having problems displaying proteins with unusual residue
>>>>> numbering, such as proteins with propeptides. An example is
>>>>
>>>> 1cs8, which
>>>>
>>>>> starts off like
>>>>> this:
>>>>>
>>>>> ATOM 1 N SER A 1P -32.762 23.978 22.929 0.00 34.26
>>>>> N
>>>>> ATOM 2 CA SER A 1P -32.360 24.645 21.660 0.00 34.08
>>>>> C
>>>>> ATOM 3 C SER A 1P -32.303 26.162 21.821 0.00 33.91
>>>>> C
>>>>> ATOM 4 O SER A 1P -32.838 26.712 22.786 0.00 33.82
>>>>> O
>>>>> ATOM 5 CB SER A 1P -33.338 24.274 20.541 0.00 34.28
>>>>> C
>>>>> ATOM 6 OG SER A 1P -34.684 24.406 20.971 0.00 34.36
>>>>> O
>>>>> .
>>>>> .
>>>>> .
>>>>> And later on comes the sequence corresponding to the
>> mature protein:
>>>>>
>>>>> ATOM 1060 N ALA A 1 11.470 66.852 16.148 1.00 22.69
>>>>> N
>>>>> ATOM 1061 CA ALA A 1 11.282 65.561 15.491 1.00 20.80
>>>>> C
>>>>> ATOM 1062 C ALA A 1 10.621 65.677 14.113 1.00 20.33
>>>>> C
>>>>> ATOM 1063 O ALA A 1 9.920 66.649 13.835 1.00 18.43
>>>>> O
>>>>> ATOM 1064 CB ALA A 1 10.451 64.636 16.393 1.00 19.50
>>>>> C
>>>>> Etc.
>>>>>
>>>>> If I open 1cs8 with PyMol, I can see everything in the "lines",
>>>>> "sticks" and "surface" representation, but in ribbon or
>> cartoon mode
>>>>> only part of the protein is shown. What do I have to do to
>>>>
>>>> show the whole sequence?
>>>>
>>>>> How do I select residues with a "P" appended to the residue
>>>>
>>>> number? If
>>>>
>>>>> I say "select resi 1P-5P" I get both 1P-5P and 1-5.
>>>>>
>>>>> Any help will be appreciated! (I am using PyMol version 0.98
>>>>
>>>> for Windows).
>>>>
>>>>> - Anne
>>>>>
>>>>> --------------------------------------------
>>>>> Anne M=F8lgaard, Ph.D.
>>>>> Center for Biological Sequence Analysis BioCentrum-DTU,
>> Building 208
>>>>> DK-2800 Lyngby
>>>>>
>>>>> Email: an...@cb...
>>>>> Phone: (+45)4525 2472
>>>>> --------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> This SF.Net email is sponsored by the JBoss Inc. Get
>> Certified Today
>>>>> Register for a JBoss Training Course. Free Certification Exam for
>>>>> All Training Attendees Through End of 2005. For more info visit:
>>>>> http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list
>>>>> PyM...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> Joel Tyndall, PhD
>>>>
>>>> Lecturer
>>>> National School of Pharmacy
>>>> University of Otago
>>>> PO Box 913 Dunedin
>>>> New Zealand
>>>>
>>>> Pukenga
>>>> Te Kura Taiwhanga Putaiao
>>>> Te Whare Wananga o Otago
>>>> Pouaka Poutapeta 913 Otepoti
>>>> Aotearoa
>>>>
>>>> Ph / Waea +64 3 4797293
>>>> Fax / Waeawhakaahua +64 3 4797034
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by the JBoss Inc. Get
>> Certified Today
>>>> Register for a JBoss Training Course. Free Certification
>> Exam for All
>>>> Training Attendees Through End of 2005. For more info visit:
>>>> http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> PyM...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by the JBoss Inc. Get
>> Certified Today
>>> Register for a JBoss Training Course. Free Certification
>> Exam for All
>>> Training Attendees Through End of 2005. For more info visit:
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>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by the JBoss Inc. Get
>> Certified Today Register for a JBoss Training Course. Free
>> Certification Exam for All Training Attendees Through End of
>> 2005. For more info visit:
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>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc. Get Certified Today
> Register for a JBoss Training Course. Free Certification Exam
> for All Training Attendees Through End of 2005. For more info visit:
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> |
|
From: <an...@cb...> - 2005-11-18 08:42:50
|
Thanks for the comments. The "retain_order" setting solves the problem = with cartoons and ribbons, but there is still a small problem with selection = of these residues. "select resi 1P-5P" still gives me both 1-5 and 1P-5P. However, "select resi 1P+2P+3P+4P+5P" gives me what I want. =20 I don't really want to change the chain ID in the PDB file. It makes = sort of sense in the case of a propeptide (although it is covalently linked to = the mature protein, so it is really only one chain), but many PDB files have insertions which are numbered with "A"s and "B"s after the residue = number, and in those cases it really doesn't make sense to change the chain ID. = For an example, see 1cgh below.=20 Thanks for your help! - Anne ATOM 213 OE1 GLN A 36 8.532 36.321 21.186 0.00 25.64 O =20 ATOM 214 NE2 GLN A 36 7.727 36.504 19.104 0.00 25.95 N =20 ATOM 215 H GLN A 36 8.523 31.138 18.943 0.00 20.00 H =20 ATOM 216 1HE2 GLN A 36 7.711 37.475 19.199 0.00 20.00 H =20 ATOM 217 2HE2 GLN A 36 7.446 36.036 18.288 0.00 20.00 H =20 ATOM 218 N SER A 36A 4.622 31.686 20.477 0.00 27.20 N =20 ATOM 219 CA SER A 36A 3.235 31.238 20.479 0.00 28.70 C =20 ATOM 220 C SER A 36A 2.315 32.417 20.162 0.00 29.65 C =20 ATOM 221 O SER A 36A 2.664 33.569 20.429 0.00 30.07 O =20 ATOM 222 CB SER A 36A 2.878 30.647 21.845 0.00 28.71 C =20 ATOM 223 OG SER A 36A 3.565 29.428 22.077 0.00 29.15 O =20 ATOM 224 H SER A 36A 5.000 32.029 21.306 0.00 20.00 H =20 ATOM 225 HG SER A 36A 4.526 29.487 22.051 0.00 20.00 H =20 ATOM 226 N PRO A 36B 1.124 32.146 19.598 0.00 30.41 N =20 ATOM 227 CA PRO A 36B 0.593 30.825 19.240 0.00 31.02 C =20 ATOM 228 C PRO A 36B 1.323 30.182 18.061 0.00 31.62 C =20 ATOM 229 O PRO A 36B 2.169 30.814 17.426 0.00 31.58 O =20 ATOM 230 CB PRO A 36B -0.867 31.125 18.914 0.00 30.83 C =20 ATOM 231 CG PRO A 36B -0.789 32.492 18.316 0.00 30.95 C =20 ATOM 232 CD PRO A 36B 0.147 33.200 19.269 0.00 30.41 C =20 ATOM 233 N ALA A 37 0.991 28.925 17.777 0.00 32.51 N =20 ATOM 234 CA ALA A 37 1.608 28.191 16.677 0.00 33.56 C =20 -------------------------------------------- Anne M=F8lgaard, Ph.D. Center for Biological Sequence Analysis BioCentrum-DTU, Building 208 DK-2800 Lyngby Email: an...@cb...=20 Phone: (+45)4525 2472 --------------------------------------------=20 -----Original Message----- From: Warren DeLano [mailto:wa...@de...]=20 Sent: 18. november 2005 02:28 To: Joel Tyndall; Anne M=F8lgaard; pym...@li... Subject: RE: [PyMOL] displaying protein with propeptide A quick fix is to use the "retain_order" setting. set retain_order which will force PyMOL to honor the order of ATOMs in the PDB file over = the numeric ordering of residue identifiers. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Joel Tyndall > Sent: Thursday, November 17, 2005 12:15 PM > To: Anne M=F8lgaard; pym...@li... > Subject: Re: [PyMOL] displaying protein with propeptide >=20 > Hi Ann, >=20 > I would change the chain id of the propeptide in a text=20 > editor, to say P and remove the P from after the residue numbers. >=20 > J >=20 > Anne M=F8lgaard wrote: >=20 > >Hi, > > > >I am having problems displaying proteins with unusual residue=20 > >numbering, such as proteins with propeptides. An example is=20 > 1cs8, which=20 > >starts off like > >this: > > > >ATOM 1 N SER A 1P -32.762 23.978 22.929 0.00 34.26 > >N =20 > >ATOM 2 CA SER A 1P -32.360 24.645 21.660 0.00 34.08 > >C =20 > >ATOM 3 C SER A 1P -32.303 26.162 21.821 0.00 33.91 > >C =20 > >ATOM 4 O SER A 1P -32.838 26.712 22.786 0.00 33.82 > >O =20 > >ATOM 5 CB SER A 1P -33.338 24.274 20.541 0.00 34.28 > >C =20 > >ATOM 6 OG SER A 1P -34.684 24.406 20.971 0.00 34.36 > >O > >. > >. > >. > >And later on comes the sequence corresponding to the mature protein: > > > >ATOM 1060 N ALA A 1 11.470 66.852 16.148 1.00 22.69 > >N =20 > >ATOM 1061 CA ALA A 1 11.282 65.561 15.491 1.00 20.80 > >C =20 > >ATOM 1062 C ALA A 1 10.621 65.677 14.113 1.00 20.33 > >C =20 > >ATOM 1063 O ALA A 1 9.920 66.649 13.835 1.00 18.43 > >O =20 > >ATOM 1064 CB ALA A 1 10.451 64.636 16.393 1.00 19.50 > >C > >Etc.=20 > > > >If I open 1cs8 with PyMol, I can see everything in the "lines",=20 > >"sticks" and "surface" representation, but in ribbon or cartoon mode=20 > >only part of the protein is shown. What do I have to do to=20 > show the whole sequence? > > > >How do I select residues with a "P" appended to the residue=20 > number? If=20 > >I say "select resi 1P-5P" I get both 1P-5P and 1-5. > > > >Any help will be appreciated! (I am using PyMol version 0.98=20 > for Windows). > > > >- Anne > > > >-------------------------------------------- > >Anne M=F8lgaard, Ph.D. > >Center for Biological Sequence Analysis BioCentrum-DTU, Building 208=20 > >DK-2800 Lyngby > > > >Email: an...@cb... > >Phone: (+45)4525 2472 > >-------------------------------------------- > > > > > > > > > >------------------------------------------------------- > >This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > >Register for a JBoss Training Course. Free Certification Exam > >for All Training Attendees Through End of 2005. For more info visit: > >http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick > >_______________________________________________ > >PyMOL-users mailing list > >PyM...@li... > >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > =20 > > >=20 > --=20 > Joel Tyndall, PhD >=20 > Lecturer > National School of Pharmacy > University of Otago > PO Box 913 Dunedin > New Zealand =20 >=20 > Pukenga > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 913 Otepoti > Aotearoa >=20 > Ph / Waea +64 3 4797293=20 > Fax / Waeawhakaahua +64 3 4797034 >=20 >=20 >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
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From: Warren D. <wa...@de...> - 2005-11-18 20:23:52
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Anne, > "select resi 1P-5P" still gives me both 1-5 and 1P-5P. > However, "select resi 1P+2P+3P+4P+5P" gives me what I want. =20 Say you have residues 36, 37A, 37B, and 38, and you tell PyMOL you wish = to select residues in the range 36-38. Naturally, you'd want 37A and = 37B included in that. It is this behavior that gives rise to the = selection behavior you've noted above, wherein residue insertion codes = are effectively ignored inside numerical ranges. =20 In PyMOL, ranges are defined numerically for reasons of performance. = Defining them based on peptide connectivity would be orders of magnitude = slower. Defining them based on their input file order could give okay = performance, but the concept of input order is not always valid given = that molecules are graphs not lists. I agree though, that it would be nice to equip PyMOL with these = alternate ranging concepts -- ideas for the future. Fortunately, there is another workaround: segment identifiers. With = wildcard selection in PyMOL beta builds, you can do something like this: alter resi *B, segi=3D'SEG1' alter not resi *B, segi=3D'SEG2' Now you could use ranges without trouble, leaving your chain IDs = unperturbed. select segi SEG1 and resi 1-5 or more concisely: select SEG1//1-5/ as distinct from select SEG2//1-5/ > but many PDB files have insertions which are numbered with "A"s and = "B"s after the residue number, As for insertion codes that appear at the proper location in sequence = (NOT the case with pathological PDB 1cs8), recent PyMOL betas handle = such situations automatically and will draw connected cartoons.=20 Cheers, Warren Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Anne M=F8lgaard > Sent: Friday, November 18, 2005 12:47 AM > To: pym...@li... > Subject: RE: [PyMOL] displaying protein with propeptide >=20 > Thanks for the comments. The "retain_order" setting solves=20 > the problem with cartoons and ribbons, but there is still a=20 > small problem with selection of these residues. "select resi=20 > 1P-5P" still gives me both 1-5 and 1P-5P. > However, "select resi 1P+2P+3P+4P+5P" gives me what I want. =20 >=20 > I don't really want to change the chain ID in the PDB file.=20 > It makes sort of sense in the case of a propeptide (although=20 > it is covalently linked to the mature protein, so it is=20 > really only one chain), but many PDB files have insertions=20 > which are numbered with "A"s and "B"s after the residue=20 > number, and in those cases it really doesn't make sense to=20 > change the chain ID. For an example, see 1cgh below.=20 >=20 > Thanks for your help! >=20 > - Anne >=20 > ATOM 213 OE1 GLN A 36 8.532 36.321 21.186 0.00 25.64 > O =20 > ATOM 214 NE2 GLN A 36 7.727 36.504 19.104 0.00 25.95 > N =20 > ATOM 215 H GLN A 36 8.523 31.138 18.943 0.00 20.00 > H =20 > ATOM 216 1HE2 GLN A 36 7.711 37.475 19.199 0.00 20.00 > H =20 > ATOM 217 2HE2 GLN A 36 7.446 36.036 18.288 0.00 20.00 > H =20 > ATOM 218 N SER A 36A 4.622 31.686 20.477 0.00 27.20 > N =20 > ATOM 219 CA SER A 36A 3.235 31.238 20.479 0.00 28.70 > C =20 > ATOM 220 C SER A 36A 2.315 32.417 20.162 0.00 29.65 > C =20 > ATOM 221 O SER A 36A 2.664 33.569 20.429 0.00 30.07 > O =20 > ATOM 222 CB SER A 36A 2.878 30.647 21.845 0.00 28.71 > C =20 > ATOM 223 OG SER A 36A 3.565 29.428 22.077 0.00 29.15 > O =20 > ATOM 224 H SER A 36A 5.000 32.029 21.306 0.00 20.00 > H =20 > ATOM 225 HG SER A 36A 4.526 29.487 22.051 0.00 20.00 > H =20 > ATOM 226 N PRO A 36B 1.124 32.146 19.598 0.00 30.41 > N =20 > ATOM 227 CA PRO A 36B 0.593 30.825 19.240 0.00 31.02 > C =20 > ATOM 228 C PRO A 36B 1.323 30.182 18.061 0.00 31.62 > C =20 > ATOM 229 O PRO A 36B 2.169 30.814 17.426 0.00 31.58 > O =20 > ATOM 230 CB PRO A 36B -0.867 31.125 18.914 0.00 30.83 > C =20 > ATOM 231 CG PRO A 36B -0.789 32.492 18.316 0.00 30.95 > C =20 > ATOM 232 CD PRO A 36B 0.147 33.200 19.269 0.00 30.41 > C =20 > ATOM 233 N ALA A 37 0.991 28.925 17.777 0.00 32.51 > N =20 > ATOM 234 CA ALA A 37 1.608 28.191 16.677 0.00 33.56 > C =20 >=20 > -------------------------------------------- > Anne M=F8lgaard, Ph.D. > Center for Biological Sequence Analysis > BioCentrum-DTU, Building 208 > DK-2800 Lyngby >=20 > Email: an...@cb... > Phone: (+45)4525 2472 > --------------------------------------------=20 >=20 > -----Original Message----- > From: Warren DeLano [mailto:wa...@de...] > Sent: 18. november 2005 02:28 > To: Joel Tyndall; Anne M=F8lgaard; pym...@li... > Subject: RE: [PyMOL] displaying protein with propeptide >=20 > A quick fix is to use the "retain_order" setting. >=20 > set retain_order >=20 > which will force PyMOL to honor the order of ATOMs in the PDB=20 > file over the numeric ordering of residue identifiers. >=20 > Cheers, > Warren >=20 > -- > Warren L. DeLano, Ph.D. =20 > Principal Scientist >=20 > . DeLano Scientific LLC =20 > . 400 Oyster Point Blvd., Suite 213 =20 > . South San Francisco, CA 94080 USA =20 > . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:wa...@de... =20 > =20 >=20 > > -----Original Message----- > > From: pym...@li... > > [mailto:pym...@li...] On Behalf Of Joel=20 > > Tyndall > > Sent: Thursday, November 17, 2005 12:15 PM > > To: Anne M=F8lgaard; pym...@li... > > Subject: Re: [PyMOL] displaying protein with propeptide > >=20 > > Hi Ann, > >=20 > > I would change the chain id of the propeptide in a text=20 > editor, to say=20 > > P and remove the P from after the residue numbers. > >=20 > > J > >=20 > > Anne M=F8lgaard wrote: > >=20 > > >Hi, > > > > > >I am having problems displaying proteins with unusual residue=20 > > >numbering, such as proteins with propeptides. An example is > > 1cs8, which > > >starts off like > > >this: > > > > > >ATOM 1 N SER A 1P -32.762 23.978 22.929 0.00 34.26 > > >N =20 > > >ATOM 2 CA SER A 1P -32.360 24.645 21.660 0.00 34.08 > > >C =20 > > >ATOM 3 C SER A 1P -32.303 26.162 21.821 0.00 33.91 > > >C =20 > > >ATOM 4 O SER A 1P -32.838 26.712 22.786 0.00 33.82 > > >O =20 > > >ATOM 5 CB SER A 1P -33.338 24.274 20.541 0.00 34.28 > > >C =20 > > >ATOM 6 OG SER A 1P -34.684 24.406 20.971 0.00 34.36 > > >O > > >. > > >. > > >. > > >And later on comes the sequence corresponding to the=20 > mature protein: > > > > > >ATOM 1060 N ALA A 1 11.470 66.852 16.148 1.00 22.69 > > >N =20 > > >ATOM 1061 CA ALA A 1 11.282 65.561 15.491 1.00 20.80 > > >C =20 > > >ATOM 1062 C ALA A 1 10.621 65.677 14.113 1.00 20.33 > > >C =20 > > >ATOM 1063 O ALA A 1 9.920 66.649 13.835 1.00 18.43 > > >O =20 > > >ATOM 1064 CB ALA A 1 10.451 64.636 16.393 1.00 19.50 > > >C > > >Etc.=20 > > > > > >If I open 1cs8 with PyMol, I can see everything in the "lines",=20 > > >"sticks" and "surface" representation, but in ribbon or=20 > cartoon mode=20 > > >only part of the protein is shown. What do I have to do to > > show the whole sequence? > > > > > >How do I select residues with a "P" appended to the residue > > number? If > > >I say "select resi 1P-5P" I get both 1P-5P and 1-5. > > > > > >Any help will be appreciated! (I am using PyMol version 0.98 > > for Windows). > > > > > >- Anne > > > > > >-------------------------------------------- > > >Anne M=F8lgaard, Ph.D. > > >Center for Biological Sequence Analysis BioCentrum-DTU,=20 > Building 208=20 > > >DK-2800 Lyngby > > > > > >Email: an...@cb... > > >Phone: (+45)4525 2472 > > >-------------------------------------------- > > > > > > > > > > > > > > >------------------------------------------------------- > > >This SF.Net email is sponsored by the JBoss Inc. Get=20 > Certified Today=20 > > >Register for a JBoss Training Course. Free Certification Exam for=20 > > >All Training Attendees Through End of 2005. For more info visit: > > >http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick > > >_______________________________________________ > > >PyMOL-users mailing list > > >PyM...@li... > > >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > =20 > > > > >=20 > > -- > > Joel Tyndall, PhD > >=20 > > Lecturer > > National School of Pharmacy > > University of Otago > > PO Box 913 Dunedin > > New Zealand =20 > >=20 > > Pukenga > > Te Kura Taiwhanga Putaiao > > Te Whare Wananga o Otago > > Pouaka Poutapeta 913 Otepoti > > Aotearoa > >=20 > > Ph / Waea +64 3 4797293=20 > > Fax / Waeawhakaahua +64 3 4797034 > >=20 > >=20 > >=20 > >=20 > >=20 > > ------------------------------------------------------- > > This SF.Net email is sponsored by the JBoss Inc. Get=20 > Certified Today=20 > > Register for a JBoss Training Course. Free Certification=20 > Exam for All=20 > > Training Attendees Through End of 2005. For more info visit: > > http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > >=20 > >=20 > >=20 > >=20 >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get=20 > Certified Today Register for a JBoss Training Course. Free=20 > Certification Exam for All Training Attendees Through End of=20 > 2005. For more info visit: > http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
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From: Eric Z. <zo...@ca...> - 2005-11-18 01:31:55
|
Is there a similar command to force PyMOL to use only CONECT lines in=20 the pdb file instead of generating connectivity by distance? Eric Warren DeLano wrote: > A quick fix is to use the "retain_order" setting. >=20 > set retain_order >=20 > which will force PyMOL to honor the order of ATOMs in the PDB file over= the numeric ordering of residue identifiers. >=20 > Cheers, > Warren >=20 > -- > Warren L. DeLano, Ph.D. =20 > Principal Scientist >=20 > . DeLano Scientific LLC =20 > . 400 Oyster Point Blvd., Suite 213 =20 > . South San Francisco, CA 94080 USA =20 > . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:wa...@de... =20 > =20 >=20 >=20 >>-----Original Message----- >>From: pym...@li...=20 >>[mailto:pym...@li...] On Behalf Of=20 >>Joel Tyndall >>Sent: Thursday, November 17, 2005 12:15 PM >>To: Anne M=F8lgaard; pym...@li... >>Subject: Re: [PyMOL] displaying protein with propeptide >> >>Hi Ann, >> >>I would change the chain id of the propeptide in a text=20 >>editor, to say P and remove the P from after the residue numbers. >> >>J >> >>Anne M=F8lgaard wrote: >> >> >>>Hi, >>> >>>I am having problems displaying proteins with unusual residue=20 >>>numbering, such as proteins with propeptides. An example is=20 >> >>1cs8, which=20 >> >>>starts off like >>>this: >>> >>>ATOM 1 N SER A 1P -32.762 23.978 22.929 0.00 34.26 >>>N =20 >>>ATOM 2 CA SER A 1P -32.360 24.645 21.660 0.00 34.08 >>>C =20 >>>ATOM 3 C SER A 1P -32.303 26.162 21.821 0.00 33.91 >>>C =20 >>>ATOM 4 O SER A 1P -32.838 26.712 22.786 0.00 33.82 >>>O =20 >>>ATOM 5 CB SER A 1P -33.338 24.274 20.541 0.00 34.28 >>>C =20 >>>ATOM 6 OG SER A 1P -34.684 24.406 20.971 0.00 34.36 >>>O >>>. >>>. >>>. >>>And later on comes the sequence corresponding to the mature protein: >>> >>>ATOM 1060 N ALA A 1 11.470 66.852 16.148 1.00 22.69 >>>N =20 >>>ATOM 1061 CA ALA A 1 11.282 65.561 15.491 1.00 20.80 >>>C =20 >>>ATOM 1062 C ALA A 1 10.621 65.677 14.113 1.00 20.33 >>>C =20 >>>ATOM 1063 O ALA A 1 9.920 66.649 13.835 1.00 18.43 >>>O =20 >>>ATOM 1064 CB ALA A 1 10.451 64.636 16.393 1.00 19.50 >>>C >>>Etc.=20 >>> >>>If I open 1cs8 with PyMol, I can see everything in the "lines",=20 >>>"sticks" and "surface" representation, but in ribbon or cartoon mode=20 >>>only part of the protein is shown. What do I have to do to=20 >> >>show the whole sequence? >> >>>How do I select residues with a "P" appended to the residue=20 >> >>number? If=20 >> >>>I say "select resi 1P-5P" I get both 1P-5P and 1-5. >>> >>>Any help will be appreciated! (I am using PyMol version 0.98=20 >> >>for Windows). >> >>>- Anne >>> >>>-------------------------------------------- >>>Anne M=F8lgaard, Ph.D. >>>Center for Biological Sequence Analysis BioCentrum-DTU, Building 208=20 >>>DK-2800 Lyngby >>> >>>Email: an...@cb... >>>Phone: (+45)4525 2472 >>>-------------------------------------------- >>> >>> >>> >>> >>>------------------------------------------------------- >>>This SF.Net email is sponsored by the JBoss Inc. Get Certified Today >>>Register for a JBoss Training Course. Free Certification Exam >>>for All Training Attendees Through End of 2005. For more info visit: >>>http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick >>>_______________________________________________ >>>PyMOL-users mailing list >>>PyM...@li... >>>https://lists.sourceforge.net/lists/listinfo/pymol-users >>> >>>=20 >>> >> >>--=20 >>Joel Tyndall, PhD >> >>Lecturer >>National School of Pharmacy >>University of Otago >>PO Box 913 Dunedin >>New Zealand =20 >> >>Pukenga >>Te Kura Taiwhanga Putaiao >>Te Whare Wananga o Otago >>Pouaka Poutapeta 913 Otepoti >>Aotearoa >> >>Ph / Waea +64 3 4797293=20 >>Fax / Waeawhakaahua +64 3 4797034 >> >> >> >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by the JBoss Inc. Get Certified Today >>Register for a JBoss Training Course. Free Certification Exam >>for All Training Attendees Through End of 2005. For more info visit: >>http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick >>_______________________________________________ >>PyMOL-users mailing list >>PyM...@li... >>https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> >> >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
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