date:20200615

[PyMOL] Antwort: PyMOL-users Digest, Vol 169, Issue 20

2020-06-15 Thread honegger



-pymol-users-requ...@lists.sourceforge.net schrieb: -
An: pymol-users@lists.sourceforge.net
Von: pymol-users-requ...@lists.sourceforge.net
Datum: 15.06.2020 22:47
Betreff: PyMOL-users Digest, Vol 169, Issue 20

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Today's Topics:

   1. Re: renumber (Mooers, Blaine H.M.  (HSC))
   2. Re: renumber (Jared Sampson)


--

Message: 1
Date: Mon, 15 Jun 2020 20:11:22 +
From: "Mooers, Blaine H.M.  (HSC)" 
To: "Oganesyan, Vaheh" , Jared
Sampson 
Cc: "pymol-users@lists.sourceforge.net"

Subject: Re: [PyMOL] renumber
Message-ID:
<87dcc6c40b22804192b6892e6429ec5fdbefd...@countach.hsc.net.ou.edu>
Content-Type: text/plain; charset="Windows-1252"

Hi Vaheh,

I susoect that your issue is an edge case for PyMOL.
The resi variable is limited to integers (see 
https://pymolwiki.org/index.php/Property_Selectors).
Atoms with letters in the resi field are invisible to PyMOL.

You could write a python script to preprocess the coordinates, run the script 
from within PyMOL, and  then reload the modified coordinates into PyMOL.
It might be more expedient to use pdb_set from ccp4, 
antibody_numbering_converter.macosclangrelease in rosetta, or biopython.

Best regards,

Blaine


PS Half of our students work in OMRF labs. Our interactions with OMRF are as 
close as ever.


Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 2:57 PM
To: Jared Sampson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Jared,

Are you saying it cannot be done within PyMOL? The ccp4 option is well known.

Thanks.

From: Jared Sampson 
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hi Vaheh -

Try `pdbset` from the CCP4 suite.

http://www.ccp4.ac.uk/html/pdbset.html#renumber

```
pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
renum 1 chain H
renum 1 chain L
end
EOF
```

Hope that helps.

Cheers,
Jared


From: Oganesyan, Vaheh 

Reply: Oganesyan, Vaheh 

Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) 
, Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net 

Subject:  Re: [PyMOL] renumber


Blain,

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

Thank you.

From: Mooers, Blaine H.M. (HSC) 
mailto:blaine-moo...@ouhsc.edu>>
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>; 
Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol

Re: [PyMOL] Renumber

2020-06-15 Thread honegger

Hello Vaheh

Antibody structures are a mess to renumber, both due to the many different
numbering schemes used in different structures, and to some older files not
even adhering to pub standards, using the alternative localisation columns for
the insertion letters specified by Kabat or Chothia nomenclature. That's why I
titled my own contribution to the mess "Yet another numbering scheme ..."

https://www.researchgate.net/publication/2530255_Yet_Another_Numbering_Scheme_for_Immunoglobulin_Variable_Domains_An_Automatic_Modeling_and_Analysis_Tool/stats

For mass renumbering of antibody variable domains, I actually use some homemade
EXCEL Visual Basic macros that extract the sequences from the coordinates into
a sequence alignment, and then renumber the pub files from the alignment.

If I had to do it in PyMOL, I would do it in multiple steps process: I would
first change the numbering to sequential numbering, allowing me to then clear
the insertion letters (resv or alt), then change the numbering to my own (AHo)
scheme by shifting the numbering of each segment by adding the appropriate
constant, starting with the most C-terminal segment to avoid problems due to
duplicate residue numbers.

I would offer to send you my macro collection, but right now I am in the middle
of fixing a number of things that broke due to the update to EXCEL 2019, so I
have to ask you for patience.

best regards

Annemarie Honegger

Hi Vaheh,

I susoect that your issue is an edge case for PyMOL.
The resi variable is limited to integers (see
https://pymolwiki.org/index.php/Property_Selectors).
Atoms with letters in the resi field are invisible to PyMOL.

You could write a python script to preprocess the coordinates, run the script
from within PyMOL, and then reload the modified coordinates into PyMOL.
It might be more expedient to use pdb_set from ccp4,
antibody_numbering_converter.macosclangrelease in rosetta, or biopython.

Best regards,

Blaine

PS Half of our students work in OMRF labs. Our interactions with OMRF are as
close as ever.

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

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Re: [PyMOL] hydrogen bond list for a series of files

2020-06-15 Thread Chen, Qiang

Thanks, Dr. Mooers.

I modified a little.

It seems the pdb files need be loaded.

I put all the following lines in a file multifile_hb.pml

run 
C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
import glob
load model.000.*_minimized.pdb
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
[cmd.do("list_hb chain F, chain A:E, 
write_distances_file=hb_"+str(file)+".txt") for file in 
glob.glob("model.000.??_minimized.pdb")]

A little not so perfect is that the output file,

hb_model.000.??_minimized.pdb.txt

Is is possible to do something like this
write_distances_file=hb_"+basename(file)+".txt"

Then the output will be
hb_model.000.??_minimized.txt

I tried, and this simple thing does not work.

Any suggestion?

Thanks!

Charles

From: Mooers, Blaine H.M. (HSC) 
Sent: Monday, June 15, 2020 9:44 PM
To: Chen, Qiang ; pymol-users@lists.sourceforge.net 

Subject: RE: hydrogen bond list for a series of files

Hi Charles,

Make sure that PyMOL's present working directory is where the pdb files are 
stored.
Copy and paste each of the four lines below one at a time on the command line 
in PyMOL.


run list_hb.py
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), 
('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", 
write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + 
"_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]

Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third 
question mark to the argument of glob.glob().

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Chen, Qiang [q...@pitt.edu]
Sent: Monday, June 15, 2020 2:53 PM
To: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files

Hi, Pymol users

Could you help me do this in an efficient way?

Let me describe the task I try to do.

I have a series of numerically ordered files, say model00.pdb model.01.pdb …… 
model.30.pdb

All the pdb have the same protein composition, chain A, B, C, D, and E. Their 
relative position is different in each file.

I would like to check the hydrogen bonds between, say, chain A and B.

Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb 
and print the list as the follows

list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt

How can I process the 30 files in an efficient way? what if I have 300 pdb 
files?

Shell script, python, or anything else?


Thanks!
Charles Chen




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Re: [PyMOL] hydrogen bond list for a series of files

2020-06-15 Thread Mooers, Blaine H.M. (HSC)

Hi Charles, 

Make sure that PyMOL's present working directory is where the pdb files are 
stored.
Copy and paste each of the four lines below one at a time on the command line 
in PyMOL.


run list_hb.py
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'), 
('B','E'), ('C','D'), ('C','E'), ('D','E') ]
[[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ", 
write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) + 
"_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]

Note that you do not have to load the pdb files into PyMOL.
If you want to analyze more than 99 files and less than 999 files, add a third 
question mark to the argument of glob.glob(). 

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Chen, Qiang [q...@pitt.edu]
Sent: Monday, June 15, 2020 2:53 PM
To: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files

Hi, Pymol users

Could you help me do this in an efficient way?

Let me describe the task I try to do.

I have a series of numerically ordered files, say model00.pdb model.01.pdb …… 
model.30.pdb

All the pdb have the same protein composition, chain A, B, C, D, and E. Their 
relative position is different in each file.

I would like to check the hydrogen bonds between, say, chain A and B.

Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb 
and print the list as the follows

list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt

How can I process the 30 files in an efficient way? what if I have 300 pdb 
files?

Shell script, python, or anything else?


Thanks!
Charles Chen




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Re: [PyMOL] renumber

2020-06-15 Thread Oganesyan, Vaheh

Thank you Jared.

From: Jared Sampson 
Sent: Monday, June 15, 2020 4:47 PM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

Hi Vaheh -

I wasn't saying it can't be done, just that pdbset is my preferred way to 
handle renumbering when going in the insertion code --> integer direction.

Within PyMOL, here is one way (you'll have to repeat for each chain you wish to 
renumber):

```
# see: 
https://pymolwiki.org/index.php/Pymol.stored
from pymol import stored

# store the current residue numbers in a list
stored.oldresi = []
iterate polymer.protein and chain L and n. CA, stored.oldresi.append(resi)

# make a list of the new residue numbers
stored.newresi = list(range(1, len(stored.oldresi)+1))

# zip them together into a lookup dict
stored.hash = dict(zip(stored.oldresi, stored.newresi))

# change the residue numbers for each atom in your chain
alter polymer.protein and chain L, resi=stored.hash[resi]
```

Hope that helps.

Cheers,
Jared

From: Oganesyan, Vaheh 

Reply: Oganesyan, Vaheh 

Date: June 15, 2020 at 3:57:24 PM
To: Jared Sampson 

Cc: pymol-users@lists.sourceforge.net 

Subject:  RE: [PyMOL] renumber

Jared,

Are you saying it cannot be done within PyMOL? The ccp4 option is well known.

Thanks.

From: Jared Sampson 
mailto:jared.samp...@columbia.edu>>
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hi Vaheh -

Try `pdbset` from the CCP4 suite.

http://www.ccp4.ac.uk/html/pdbset.html#renumber

```
pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
renum 1 chain H
renum 1 chain L
end
EOF
```

Hope that helps.

Cheers,
Jared

From: Oganesyan, Vaheh 

Reply: Oganesyan, Vaheh 

Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) 
, Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net 

Subject:  Re: [PyMOL] renumber

Blain,

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

Thank you.

From: Mooers, Blaine H.M. (HSC) 
mailto:blaine-moo...@ouhsc.edu>>
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>; 
Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,

From: Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber

Re: [PyMOL] renumber

2020-06-15 Thread Jared Sampson

Hi Vaheh - 

I wasn't saying it can't be done, just that pdbset is my preferred way to 
handle renumbering when going in the insertion code --> integer direction.

Within PyMOL, here is one way (you'll have to repeat for each chain you wish to 
renumber):

```
# see: https://pymolwiki.org/index.php/Pymol.stored
from pymol import stored

# store the current residue numbers in a list
stored.oldresi = []
iterate polymer.protein and chain L and n. CA, stored.oldresi.append(resi)

# make a list of the new residue numbers
stored.newresi = list(range(1, len(stored.oldresi)+1))

# zip them together into a lookup dict
stored.hash = dict(zip(stored.oldresi, stored.newresi))

# change the residue numbers for each atom in your chain
alter polymer.protein and chain L, resi=stored.hash[resi]
```

Hope that helps.

Cheers,
Jared



From: Oganesyan, Vaheh 
Reply: Oganesyan, Vaheh 
Date: June 15, 2020 at 3:57:24 PM
To: Jared Sampson 
Cc: pymol-users@lists.sourceforge.net 
Subject:  RE: [PyMOL] renumber  

Jared,

 

Are you saying it cannot be done within PyMOL? The ccp4 option is well known.

 

Thanks.

 

From: Jared Sampson   
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

 

Hi Vaheh -

 

Try `pdbset` from the CCP4 suite.

 

http://www.ccp4.ac.uk/html/pdbset.html#renumber

 

```

pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF

renum 1 chain H

renum 1 chain L

end

EOF

```

 

Hope that helps.

 

Cheers,

Jared

 


From: Oganesyan, Vaheh 
Reply: Oganesyan, Vaheh 
Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) , Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net 
Subject:  Re: [PyMOL] renumber




Blain,

 

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

 

Thank you.

 

From: Mooers, Blaine H.M. (HSC)   
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh ; Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

 

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run 
renumber.py

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

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Re: [PyMOL] renumber

2020-06-15 Thread Mooers, Blaine H.M. (HSC)

Hi Vaheh,

I susoect that your issue is an edge case for PyMOL.
The resi variable is limited to integers (see 
https://pymolwiki.org/index.php/Property_Selectors).
Atoms with letters in the resi field are invisible to PyMOL.

You could write a python script to preprocess the coordinates, run the script 
from within PyMOL, and  then reload the modified coordinates into PyMOL.
It might be more expedient to use pdb_set from ccp4, 
antibody_numbering_converter.macosclangrelease in rosetta, or biopython.

Best regards,

Blaine


PS Half of our students work in OMRF labs. Our interactions with OMRF are as 
close as ever.


Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 2:57 PM
To: Jared Sampson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Jared,

Are you saying it cannot be done within PyMOL? The ccp4 option is well known.

Thanks.

From: Jared Sampson 
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hi Vaheh -

Try `pdbset` from the CCP4 suite.

http://www.ccp4.ac.uk/html/pdbset.html#renumber

```
pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
renum 1 chain H
renum 1 chain L
end
EOF
```

Hope that helps.

Cheers,
Jared


From: Oganesyan, Vaheh 

Reply: Oganesyan, Vaheh 

Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) 
, Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net 

Subject:  Re: [PyMOL] renumber


Blain,

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

Thank you.

From: Mooers, Blaine H.M. (HSC) 
mailto:blaine-moo...@ouhsc.edu>>
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>; 
Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber

[PyMOL] hydrogen bond list for a series of files

2020-06-15 Thread Chen, Qiang

Hi, Pymol users

Could you help me do this in an efficient way?

Let me describe the task I try to do.

I have a series of numerically ordered files, say model00.pdb model.01.pdb …… 
model.30.pdb

All the pdb have the same protein composition, chain A, B, C, D, and E. Their 
relative position is different in each file.

I would like to check the hydrogen bonds between, say, chain A and B.

Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in one pdb 
and print the list as the follows

list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt 

How can I process the 30 files in an efficient way? what if I have 300 pdb 
files?

Shell script, python, or anything else?


Thanks!
Charles Chen




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Re: [PyMOL] renumber (Oganesyan, Vaheh)

2020-06-15 Thread Chen, Qiang



Coot is also an option.

CCP4 is much better/flexible though.
> On Jun 15, 2020, at 3:57 PM, pymol-users-requ...@lists.sourceforge.net wrote:
> 
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> 
> 
> Today's Topics:
> 
>   1. Re: renumber (Oganesyan, Vaheh)
> 
> 
> --
> 
> Message: 1
> Date: Mon, 15 Jun 2020 19:57:14 +
> From: "Oganesyan, Vaheh" 
> To: Jared Sampson 
> Cc: "pymol-users@lists.sourceforge.net"
>   
> Subject: Re: [PyMOL] renumber
> Message-ID:
>   
> 
>   
> Content-Type: text/plain; charset="utf-8"
> 
> Jared,
> 
> Are you saying it cannot be done within PyMOL? The ccp4 option is well known.
> 
> Thanks.
> 
> From: Jared Sampson 
> Sent: Monday, June 15, 2020 2:41 PM
> To: Oganesyan, Vaheh 
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] renumber
> 
> Hi Vaheh -
> 
> Try `pdbset` from the CCP4 suite.
> 
> https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ccp4.ac.uk%2Fhtml%2Fpdbset.html%23renumber&data=02%7C01%7Cqic8%40pitt.edu%7C1cb5bc4305a54e41116508d811666261%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637278478724651262&sdata=xdDIHjozZKMKwAR4hQiO9ghd%2FMXaqmFpSfwkZRJ4r9w%3D&reserved=0
> 
> ```
> pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
> renum 1 chain H
> renum 1 chain L
> end
> EOF
> ```
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> 
> From: Oganesyan, Vaheh 
> 
> Reply: Oganesyan, Vaheh 
> 
> Date: June 15, 2020 at 1:28:23 PM
> To: Mooers, Blaine H.M. (HSC) 
> , Jarrett Johnson 
> 
> Cc: 
> pymol-users@lists.sourceforge.net 
> 
> Subject:  Re: [PyMOL] renumber
> 
> 
> Blain,
> 
> The command will not change the numbering of amino acids starting from #1. 
> But if you got missing ones, like in my case, it will. Except for those 
> having also letter in the number field. I mean the numbering used for CDRs of 
> antibodies, not alternatives. Hence, my question, is there a command that 
> will ignore the letters in the number field and renumber the amino acids in 
> the order they appear in the file.
> 
> Thank you.
> 
> From: Mooers, Blaine H.M. (HSC) 
> mailto:blaine-moo...@ouhsc.edu>>
> Sent: Monday, June 15, 2020 12:06 PM
> To: Oganesyan, Vaheh 
> mailto:vaheh.oganes...@astrazeneca.com>>; 
> Jarrett Johnson 
> mailto:jarrett.john...@schrodinger.com>>
> Cc: 
> pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] renumber
> 
> Hi Vaheh,
> 
> alter vh, resi=str(int(resi)+0)
> 
> will not change the residue numbers because 0 is being added.
> Replace 0 with your desired residue number offset.
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> 
> From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
> Sent: Monday, June 15, 2020 10:49 AM
> To: Jarrett Johnson
> Cc: 
> pymol-users@lists.sourceforge.net
> Subject: [EXTERNAL] Re: [PyMOL] renumber
> 
> Thank you Jarrett,
> 
> Then the command
> 
> alter vh, resi=str(int(resi)+0)
> 
> should work, right? But it doesn?t because there are residue numbers with 
> letters. Is there a command that will either remove the letters or won?t pay 
> attention to them and renumber sequentially.
> 
> Regards,
> 
> 
> From: Jarrett Johnson 
> mailto:jarrett.john...@schrodinger.com>>
> Sent: Monday, June 15, 2020 11:38 AM
> To: Oganesyan, Vaheh 
> m

Re: [PyMOL] renumber

2020-06-15 Thread Oganesyan, Vaheh

Jared,

Are you saying it cannot be done within PyMOL? The ccp4 option is well known.

Thanks.

From: Jared Sampson 
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hi Vaheh -

Try `pdbset` from the CCP4 suite.

http://www.ccp4.ac.uk/html/pdbset.html#renumber

```
pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
renum 1 chain H
renum 1 chain L
end
EOF
```

Hope that helps.

Cheers,
Jared

From: Oganesyan, Vaheh 

Reply: Oganesyan, Vaheh 

Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) 
, Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net 

Subject:  Re: [PyMOL] renumber

Blain,

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

Thank you.

From: Mooers, Blaine H.M. (HSC) 
mailto:blaine-moo...@ouhsc.edu>>
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>; 
Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,

From: Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber>
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run 
renumber.py>

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
 wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?

Regards,

Vaheh

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Re: [PyMOL] renumber

2020-06-15 Thread Jared Sampson

Hi Vaheh -

Try `pdbset` from the CCP4 suite.

http://www.ccp4.ac.uk/html/pdbset.html#renumber

```
pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
renum 1 chain H
renum 1 chain L
end
EOF
```

Hope that helps.

Cheers,
Jared


From: Oganesyan, Vaheh 
Reply: Oganesyan, Vaheh 
Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) , Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net 
Subject:  Re: [PyMOL] renumber  

Blain,

 

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

 

Thank you.

 

From: Mooers, Blaine H.M. (HSC)   
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh ; Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

 

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run 
renumber.py

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

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--

Jarrett Johnson | Senior Developer

[Schrodinger 
Logo]

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Re: [PyMOL] renumber

2020-06-15 Thread Mooers, Blaine H.M. (HSC)

Hi Vaheh,

Thank you for the clarification. 
There are at least five numbering schemes 
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198058).
Which one are you following?

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 12:26 PM
To: Mooers, Blaine H.M.  (HSC); Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] RE: [PyMOL] renumber

Blain,

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

Thank you.

From: Mooers, Blaine H.M. (HSC) 
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh ; Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run 
renumber.py

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
 wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

___
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Re: [PyMOL] renumber

2020-06-15 Thread Oganesyan, Vaheh

Blain,

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

Thank you.

From: Mooers, Blaine H.M. (HSC) 
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh ; Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn't because there are residue numbers with 
letters. Is there a command that will either remove the letters or won't pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber>
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run 
renumber.py>

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
 wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn't 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

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Re: [PyMOL] renumber

2020-06-15 Thread Mooers, Blaine H.M. (HSC)

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page  
https://pymolwiki.org/index.php/Renumber
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run 
renumber.py

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

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Logo]




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Re: [PyMOL] renumber

2020-06-15 Thread Oganesyan, Vaheh

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page  
https://pymolwiki.org/index.php/Renumber
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run renumber.py

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

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--

Jarrett Johnson | Senior Developer
[Schrodinger Logo]

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Re: [PyMOL] renumber

2020-06-15 Thread Jarrett Johnson

Hello,

The command shown on this page  https://pymolwiki.org/index.php/Renumber is
not one that comes with PyMOL by default. Try downloading the script and
importing it via the `run` command in the PyMOL command-line:

*run renumber.py*

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh <
vaheh.oganes...@astrazeneca.com> wrote:

>
>
> Hello PyMOLers,
>
>
>
> Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t
> recognize it. Is it that Wiki is old, or my PyMOL version is dusty?
>
>
>
>
>
> Regards,
>
>
>
> Vaheh
>
>
> ___
> PyMOL-users mailing list
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> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] 
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[PyMOL] renumber

2020-06-15 Thread Oganesyan, Vaheh


Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn't 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

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Re: [PyMOL] User data

2020-06-15 Thread Thomas Holder

Hi Pedro,

There is no designated infrastructure for this. Other plugins typically create 
their own directory in the user's home folder, like "~/.myplugindata". You 
could also create it inside the "~/.pymol" directory (like 
"~/.pymol/myplugindata").

This works on all platforms:
os.path.expanduser("~/.pymol/myplugindata")

On Windows, you could also put it inside the %APPDATA% directory:
os.path.join(os.environ['APPDATA'], 'pymol', 'myplugindata')


Let me know how you decide or if you have other ideas!

Cheers,
  Thomas


> On Jun 9, 2020, at 10:20 PM, Pedro Lacerda  wrote:
> 
> Hi PyMOL users and developers,
> 
> I have a plugin that needs to download data periodically. Where should I 
> download to?
> 
> By the way, I managed to get a plugin into a python package.
> 
> https://github.com/pslacerda/pymol-labimm/blob/master/scripts/pymol_labimm.py
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] APBS plugin for Sugars

2020-06-15 Thread Thomas Holder

Hi Mario,

Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to 
manually edit the files there as well. For example with PyMOL 2.4.0 on Linux, 
the AMBER force field data files can be found like this:

$ find . -name "AMBER.*"
./lib/python3.7/site-packages/src/dat/AMBER.names
./lib/python3.7/site-packages/src/dat/AMBER.DAT


Hope that helps.

Cheers,
  Thomas


> On Jun 14, 2020, at 6:35 PM, Mario Garcia Urena  wrote:
> 
> Hi all,
>  
> I was trying to generate dipole moments with pymol using the APBS plugin. For 
> proteins I adapted a code and the dipole moments are correct and work just 
> fine, but for sugars it does not. I am well aware that the problem is that 
> many of the residues are not present in the AMBER force field data (or the 
> force field I want to use.) In APBS it is relatively easy to adapt and 
> introduce the sugars’ information manually, however in the APBS plugin for 
> pymol gets a little bit thorny. I cannot seem to find the files where I 
> should store the sugar information. Has anybody done this before? Any 
> alternatives with other programs or approaches are also welcome.
>  
> Thank you in advance,
>  
> Mario
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Schrödinger, Inc.



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[PyMOL] Antwort: PyMOL-users Digest, Vol 169, Issue 20

Re: [PyMOL] Renumber

Re: [PyMOL] hydrogen bond list for a series of files

Re: [PyMOL] hydrogen bond list for a series of files

Re: [PyMOL] renumber

Re: [PyMOL] renumber

Re: [PyMOL] renumber

[PyMOL] hydrogen bond list for a series of files

Re: [PyMOL] renumber (Oganesyan, Vaheh)

Re: [PyMOL] renumber

Re: [PyMOL] renumber

Re: [PyMOL] renumber

Re: [PyMOL] renumber

Re: [PyMOL] renumber

Re: [PyMOL] renumber

Re: [PyMOL] renumber

[PyMOL] renumber

Re: [PyMOL] User data

Re: [PyMOL] APBS plugin for Sugars

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