BS"D
Dear All,
I thought I saw something about using get_area to get a residue by residue
value for solvent accessible surface area, instead of the a per atom list. But
I can't seem to find that now. Any ideas?
In relation to this, when using the load_b option, can one redirect the outpu
Dear Sir/Madam
I have generated five models for a protein and I wanted to check how the
models align to each other and color them by RMSD/RMSF. I wanted to know
what should be the ideal way to do it. Shall I use RMSF or RMSD for the
same?
I tried doing this using rmsf_states.py and color_b.py scri
Hej Harry,
This PyMOL wiki page may help you out further, it may be hard to find
without the underscore in the name:
http://www.pymolwiki.org/index.php/Get_Area
If you use the load_b=1 option, PyMOL will overwrite the b-factor.
You could select the atom by the overwritten b-factor, e.g.:
select m
Hej Nidhi,
I'm not familiar with the two scipts but the usage appears correct. You can
check the arguments in PyMOL using e.g.:
rmsf_states ?
and/or:
help rmsf_states
I assume the color_b command is a simplification of the spectrum command,
so you could also check out:
http://www.pymolwiki.org/in
BS"D
Dear Andreas,
Thanks very much for the help
Harry
On Jul 23, 2014, at 2:34 PM, Andreas Warnecke wrote:
Hej Harry,
This PyMOL wiki page may help you out further, it may be hard to find without
the underscore in the name:
http://www.pymolwiki.org/index.php/Get_Area
If you use the
Hello Hidhi,
On Wed, 2014-07-23 16:39 EDT, Nidhi Jatana
wrote:
> Dear Sir/Madam
> I have generated five models for a protein and I wanted to check how the
> models align to each other and color them by RMSD/RMSF. I wanted to know
> what should be the ideal way to do it. Shall I use RMSF or RMS
Hi, I am using pymol from the SVN, and I have run into a problem when
using revision 4083.
When loading an sdf file of small molecules, pymol segfaults with the
following error:
/usr/local/bin/pymol: line 3: 29872 Segmentation fault (core
dumped) "/usr/bin/python"
"/usr/local/lib/python2.
Hi Matt,
thank you for the bug report. We will fix this as soon as possible.
Cheers,
Thomas
On 23 Jul 2014, at 13:06, Matthew Baumgartner wrote:
> Hi, I am using pymol from the SVN, and I have run into a problem when
> using revision 4083.
> When loading an sdf file of small molecules, pymol
Hi Matt,
I pushed a fix to SVN rev 4084.
Cheers,
Thomas
On 23 Jul 2014, at 14:06, Thomas Holder wrote:
> Hi Matt,
>
> thank you for the bug report. We will fix this as soon as possible.
>
> Cheers,
> Thomas
>
> On 23 Jul 2014, at 13:06, Matthew Baumgartner wrote:
>> Hi, I am using pymol
Is it currently possible to contour map representations (i.e. isomesh) by
absolute values (electrons per cubic angstroms) rather than by the map's sigma
value? For example, this is useful when making figures comparing maps from two
different structures.
Sincerely,
Justin T. Biel
Graduate Studen
Hi,
I have a really just awful way of doing this and was wondering if there is a
pymol solution that would make it easier.
Here is the problem.
Given two protein sequences, align their corresponding amino acids. The
position of each of the strings is not known, just the sequence.
Ex.
Protei
Hi Justin,
before loading the map, do:
PyMOL> set normalize_ccp4_maps, off
Assuming you are loading from a ccp4 map file. There is also
normalize_grd_maps and normalize_o_maps.
Cheers,
Thomas
Biel, Justin wrote, On 07/23/14 21:50:
> Is it currently possible to contour map representations (i.
Hi Jordan,
use the "pepseq" selection operator:
select align_1, protein_1 and pepseq YYDFGHSFG
select align_2, protein_2 and pepseq YYDFGHSFG
align align_1, align_2
Cheers,
Thomas
Jordan Willis wrote, On 07/23/14 21:58:
> Hi,
>
> I have a really just awful way of doing this and was wonde
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