[PyMOL] Question about rotation in latest version of Pymol

[Katayoun Etemadi Some Olyayi]

Hello,

I’m trying to rotate 2 atoms simultaneously in Pymol, mac version. I am able to 
do that by using the command: “rotate axis, angle, selection”. But any axis 
that I use, gives out very long bonds that look definitely wrong. Except for 
doing it manually, (using command key+ left click) are there any other commands 
I could use?

Thanks,
Katayoun
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Re: [PyMOL] Question on residue selection in multiple PDB

[Neena Susan Eappen]

Thank you so much Jarrett, yes it works very well!

On Thu, 20 Jul 2023 at 08:51, Jarrett Johnson <
jarrett.john...@schrodinger.com> wrote:

> Sorry, typo. For the second approach, state should be `i + 1` and not `-1`"
>
> Jarrett J.
>
> On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson <
> jarrett.john...@schrodinger.com> wrote:
>
>> Hi Neena,
>>
>> Is the split_states necessary? You can query the distance between atoms
>> on the state-level as well without having to break up your structure.
>> Here's two approaches that show either way; I recommend the second if
>> possible. You'll of course have to switch out the selection string to fit
>> your own atom pairs.
>>
>> from pymol import cmd
>>
>> # Approach 1: With splitting states
>>
>> cmd.fetch('1L2Y')
>> cmd.split_states('1L2Y')
>> for i in range(cmd.count_states('1L2Y')):
>> nmr_frame = f"1L2Y_{i + 1:04d}"
>> sele1 = f"/{nmr_frame}/A/A/ILE`4/O"
>> sele2 = f"/{nmr_frame}/A/A/ASP`9/CA"
>> dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2)
>> print(dist)
>>
>> print("")
>>
>> # Approach 2: Without splitting states
>>
>> for i in range(cmd.count_states('1L2Y')):
>> sele1 = "/1L2Y/A/A/ILE`4/O"
>> sele2 = "/1L2Y/A/A/ASP`9/CA"
>> dist = cmd.get_distance(sele1, sele2, state=-1)
>> print(dist)
>>
>>
>> Hope that helps,
>> Jarrett J
>>
>>
>> On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen <
>> neenasusan...@gmail.com> wrote:
>>
>>> Hello PyMOL users,
>>>
>>> Can I get some insight on how to approach this analysis?
>>>
>>> Many thanks,
>>> Neena
>>>
>>> On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen 
>>> wrote:
>>>
 Hello PyMOL Team,

 I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has
 38 NMR structures deposited in it.
 Using split_states command, I can see all 38 structures.
 I want to find polar contacts between same 3 residues in all these 38
 structures and extract corresponding distance values for polar contacts.

 Question: Is there a single command to select 3 residues in all these
 38 structures and find polar contacts within this selection?

 Many thanks,
 Neena

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>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>>
>> --
>>
>> *Jarrett Johnson* | Senior Developer, PyMOL
>>
>>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>
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Re: [PyMOL] Question on residue selection in multiple PDB

[Jarrett Johnson]

Sorry, typo. For the second approach, state should be `i + 1` and not `-1`"

Jarrett J.

On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson <
jarrett.john...@schrodinger.com> wrote:

> Hi Neena,
>
> Is the split_states necessary? You can query the distance between atoms on
> the state-level as well without having to break up your structure. Here's
> two approaches that show either way; I recommend the second if possible.
> You'll of course have to switch out the selection string to fit your own
> atom pairs.
>
> from pymol import cmd
>
> # Approach 1: With splitting states
>
> cmd.fetch('1L2Y')
> cmd.split_states('1L2Y')
> for i in range(cmd.count_states('1L2Y')):
> nmr_frame = f"1L2Y_{i + 1:04d}"
> sele1 = f"/{nmr_frame}/A/A/ILE`4/O"
> sele2 = f"/{nmr_frame}/A/A/ASP`9/CA"
> dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2)
> print(dist)
>
> print("")
>
> # Approach 2: Without splitting states
>
> for i in range(cmd.count_states('1L2Y')):
> sele1 = "/1L2Y/A/A/ILE`4/O"
> sele2 = "/1L2Y/A/A/ASP`9/CA"
> dist = cmd.get_distance(sele1, sele2, state=-1)
> print(dist)
>
>
> Hope that helps,
> Jarrett J
>
>
> On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen <
> neenasusan...@gmail.com> wrote:
>
>> Hello PyMOL users,
>>
>> Can I get some insight on how to approach this analysis?
>>
>> Many thanks,
>> Neena
>>
>> On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen 
>> wrote:
>>
>>> Hello PyMOL Team,
>>>
>>> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has
>>> 38 NMR structures deposited in it.
>>> Using split_states command, I can see all 38 structures.
>>> I want to find polar contacts between same 3 residues in all these 38
>>> structures and extract corresponding distance values for polar contacts.
>>>
>>> Question: Is there a single command to select 3 residues in all these 38
>>> structures and find polar contacts within this selection?
>>>
>>> Many thanks,
>>> Neena
>>>
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>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

-- 

*Jarrett Johnson* | Senior Developer, PyMOL
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Re: [PyMOL] Question on residue selection in multiple PDB

[Jarrett Johnson]

Hi Neena,

Is the split_states necessary? You can query the distance between atoms on
the state-level as well without having to break up your structure. Here's
two approaches that show either way; I recommend the second if possible.
You'll of course have to switch out the selection string to fit your own
atom pairs.

from pymol import cmd

# Approach 1: With splitting states

cmd.fetch('1L2Y')
cmd.split_states('1L2Y')
for i in range(cmd.count_states('1L2Y')):
nmr_frame = f"1L2Y_{i + 1:04d}"
sele1 = f"/{nmr_frame}/A/A/ILE`4/O"
sele2 = f"/{nmr_frame}/A/A/ASP`9/CA"
dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2)
print(dist)

print("")

# Approach 2: Without splitting states

for i in range(cmd.count_states('1L2Y')):
sele1 = "/1L2Y/A/A/ILE`4/O"
sele2 = "/1L2Y/A/A/ASP`9/CA"
dist = cmd.get_distance(sele1, sele2, state=-1)
print(dist)


Hope that helps,
Jarrett J


On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen 
wrote:

> Hello PyMOL users,
>
> Can I get some insight on how to approach this analysis?
>
> Many thanks,
> Neena
>
> On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen 
> wrote:
>
>> Hello PyMOL Team,
>>
>> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38
>> NMR structures deposited in it.
>> Using split_states command, I can see all 38 structures.
>> I want to find polar contacts between same 3 residues in all these 38
>> structures and extract corresponding distance values for polar contacts.
>>
>> Question: Is there a single command to select 3 residues in all these 38
>> structures and find polar contacts within this selection?
>>
>> Many thanks,
>> Neena
>>
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> Unsubscribe:
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Re: [PyMOL] Question on residue selection in multiple PDB

[Neena Susan Eappen]

Hello PyMOL users,

Can I get some insight on how to approach this analysis?

Many thanks,
Neena

On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen 
wrote:

> Hello PyMOL Team,
>
> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38
> NMR structures deposited in it.
> Using split_states command, I can see all 38 structures.
> I want to find polar contacts between same 3 residues in all these 38
> structures and extract corresponding distance values for polar contacts.
>
> Question: Is there a single command to select 3 residues in all these 38
> structures and find polar contacts within this selection?
>
> Many thanks,
> Neena
>
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[PyMOL] Question on residue selection in multiple PDB

[Neena Susan Eappen]

Hello PyMOL Team,

I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38
NMR structures deposited in it.
Using split_states command, I can see all 38 structures.
I want to find polar contacts between same 3 residues in all these 38
structures and extract corresponding distance values for polar contacts.

Question: Is there a single command to select 3 residues in all these 38
structures and find polar contacts within this selection?

Many thanks,
Neena
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[PyMOL] Question about formatting font size

[Chao Chen]

Dear Users,

I found in pymol layout somehow characters including protein sequence
letters become very small. Not sure what I have done. Any ideas of changing
to a bigger font? Thanks a lot in advance!

Kind regards,
Chao
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[PyMOL] Question regarding transparency

[wenchao zhang]

Dear Pymol users,

I have a question about transparency.

I would like to transparent both the cartoon and the surface to highlight
the sticks, but when I transparent both of them, the cartoon will
disappear, how do you solve this?

Thank you in advance!
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Re: [PyMOL] Question about glm in pymol

[Jarrett Johnson]

Hi,

Your version of glm (default with Centos7 with yum) should now work. I
committed a change to fix this compiler error about twelve hours ago. You
just need to pull the latest changes.

Best,

Jarrett J.

On Tue, Jul 12, 2022 at 10:24 PM 张敏华  wrote:

> Dear Jarrett Johnson：
> In fact I encountered an error message when I am installing the
> latest version of pymol.  First I installed all the library that needed
> according the pymolwiki by yum.  Then during the installation process, an
> error message appeared:
>
>“ layer0/TTT.cpp:87:27: error: no match for ‘operator=’ (operand
> types are ‘glm::vec3 {aka glm::tvec3}’ and
> ‘glm::tmat4x4::col_type {aka glm::tvec4 (glm::precision)0u>}’)
>
>result.m_pretranslation = mult[3];
>
>  
>
> error:  command 'g++’failed with exit status 1”
>
>So I guess there might be something wrong with glm, but I don't
> know how to solve it. Maybe the glm version installed by yum in CentOS7 is
> not the latest version? I searched the google and some threads suggests
> that should use the glm-0.9.9 instead yum installed glm-0.9.6. Then how to
> use the glm-0.9.9?
>
>
>
> --
> Minhua Zhang, Ph.D., Assistant Professor
> Structural Biology Lab
> Institute of Plant Physiology and Ecology, Shanghai Institute of
> Biological Sciences
> Chinese Academy of Sciences
> 300 Fenglin Road, Shanghai, 20032, P.R.China
> Tel:  86 21 5492 4218
> Fax:  86 21 5492 4015
> Email: mhzh...@sippe.ac.cn
>
>
> *From:* Jarrett Johnson 
> *Date:* 2022-07-13 00:33
> *To:* 张敏华 
> *CC:* pymol-users 
> *Subject:* Re: [PyMOL] Question about glm in pymol
> Hello,
>
> Through CentOS, you should be able to install glm with yum package manager.
>
> yum install glm-devel
>
> More info can be found here: https://pymolwiki.org/index.php/Linux_Install
> .
>
> Also take note that if you're using Centos 7, the default glm may not have
> a modern enough API for PyMOL code. I updated the codebase today which
> should make it compatible with this version of glm. Make sure to pull again
> if that's the case for you.
>
> Best,
> Jarrett J
>
> On Tue, Jul 12, 2022 at 12:26 PM 张敏华  wrote:
>
>> Dear all:
>> I want to comple open-source-pymol in CentOS. So I want to using
>> the latest glm. So how to install glm? or  I just put the glm folder into
>> the include folder in the open-sourde-pymol folder?
>>
>> --
>> Minhua Zhang, Ph.D., Assistant Professor
>> Structural Biology Lab
>> Institute of Plant Physiology and Ecology, Shanghai Institute of
>> Biological Sciences
>> Chinese Academy of Sciences
>> 300 Fenglin Road, Shanghai, 20032, P.R.China
>> Tel:  86 21 5492 4218
>> Fax:  86 21 5492 4015
>> Email: mhzh...@sippe.ac.cn
>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

-- 

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Re: [PyMOL] Question about glm in pymol

[Jarrett Johnson]

Hello,

Through CentOS, you should be able to install glm with yum package manager.

yum install glm-devel

More info can be found here: https://pymolwiki.org/index.php/Linux_Install .

Also take note that if you're using Centos 7, the default glm may not have
a modern enough API for PyMOL code. I updated the codebase today which
should make it compatible with this version of glm. Make sure to pull again
if that's the case for you.

Best,
Jarrett J

On Tue, Jul 12, 2022 at 12:26 PM 张敏华  wrote:

> Dear all:
> I want to comple open-source-pymol in CentOS. So I want to using
> the latest glm. So how to install glm? or  I just put the glm folder into
> the include folder in the open-sourde-pymol folder?
>
> --
> Minhua Zhang, Ph.D., Assistant Professor
> Structural Biology Lab
> Institute of Plant Physiology and Ecology, Shanghai Institute of
> Biological Sciences
> Chinese Academy of Sciences
> 300 Fenglin Road, Shanghai, 20032, P.R.China
> Tel:  86 21 5492 4218
> Fax:  86 21 5492 4015
> Email: mhzh...@sippe.ac.cn
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> Unsubscribe:
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Re: [PyMOL] Question about glm in pymol

[张敏华]

Dear Jarrett Johnson：
In fact I encountered an error message when I am installing the latest 
version of pymol.  First I installed all the library that needed according the 
pymolwiki by yum.  Then during the installation process, an error message 
appeared:
  
   “ layer0/TTT.cpp:87:27: error: no match for ‘operator=’ (operand types 
are ‘glm::vec3 {aka glm::tvec3}’ and 
‘glm::tmat4x4::col_type {aka glm::tvec4}’)
   result.m_pretranslation = mult[3];

 

error:  command 'g++’failed with exit status 1”

   So I guess there might be something wrong with glm, but I don't know how 
to solve it. Maybe the glm version installed by yum in CentOS7 is not the 
latest version? I searched the google and some threads suggests that should use 
the glm-0.9.9 instead yum installed glm-0.9.6. Then how to use the glm-0.9.9? 





Minhua Zhang, Ph.D., Assistant Professor
Structural Biology Lab
Institute of Plant Physiology and Ecology, Shanghai Institute of Biological 
Sciences
Chinese Academy of Sciences
300 Fenglin Road, Shanghai, 20032, P.R.China
Tel:  86 21 5492 4218
Fax:  86 21 5492 4015 
Email: mhzh...@sippe.ac.cn
 
From: Jarrett Johnson
Date: 2022-07-13 00:33
To: 张敏华
CC: pymol-users
Subject: Re: [PyMOL] Question about glm in pymol
Hello,

Through CentOS, you should be able to install glm with yum package manager.

yum install glm-devel

More info can be found here: https://pymolwiki.org/index.php/Linux_Install .

Also take note that if you're using Centos 7, the default glm may not have a 
modern enough API for PyMOL code. I updated the codebase today which should 
make it compatible with this version of glm. Make sure to pull again if that's 
the case for you. 

Best,
Jarrett J

On Tue, Jul 12, 2022 at 12:26 PM 张敏华  wrote:
Dear all:
I want to comple open-source-pymol in CentOS. So I want to using the 
latest glm. So how to install glm? or  I just put the glm folder into the 
include folder in the open-sourde-pymol folder?



Minhua Zhang, Ph.D., Assistant Professor
Structural Biology Lab
Institute of Plant Physiology and Ecology, Shanghai Institute of Biological 
Sciences
Chinese Academy of Sciences
300 Fenglin Road, Shanghai, 20032, P.R.China
Tel:  86 21 5492 4218
Fax:  86 21 5492 4015 
Email: mhzh...@sippe.ac.cn
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-- 
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[PyMOL] Question about glm in pymol

[张敏华]

Dear all:
I want to comple open-source-pymol in CentOS. So I want to using the 
latest glm. So how to install glm? or  I just put the glm folder into the 
include folder in the open-sourde-pymol folder?



Minhua Zhang, Ph.D., Assistant Professor
Structural Biology Lab
Institute of Plant Physiology and Ecology, Shanghai Institute of Biological 
Sciences
Chinese Academy of Sciences
300 Fenglin Road, Shanghai, 20032, P.R.China
Tel:  86 21 5492 4218
Fax:  86 21 5492 4015 
Email: mhzh...@sippe.ac.cn
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Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

[Ali Saad Kusay]

Hi Jeff, 

That would be cmd.disable("object name") # 
https://pymolwiki.org/index.php/Disable 

Cheers,

Ali

On 1/3/21, 9:05 pm, "Jeff Saxon"  wrote:

Thank you very much, Ali!
Yes, actually, I suppose I have set up vdw radii using those commands,
considering specific selections,e.g this is part of my pymol script
that I am using in bash.
$pymol -c -d "
from pymol import cmd

cmd.load('${storage}/${syst_name}/all_clusters.pdb')
cmd.split_states('all_clusters*')
cmd.select('all_clusters*')
cmd.show('spheres', 'sele')
cmd.set('sphere_transparency', '0.2', 'sele')
cmd.color('marine', 'sele' )
cmd.alter('all_clusters*', 'vdw=0.75')
cmd.select('all_clusters*')
cmd.show( 'spheres', 'sele' )
cmd.rebuild()
cmd.bg_color('white')
cmd.save('${syst}/${syst_name}.pse')

cmd.png('${vizu}/${syst_name}.png',width=${image},height=${image},dpi=50,ray=0)
"

Eventually in my saved pml session everything looks fine BUT on the
png image some of the spheres (notably located on the back plane in
the space) are appeared to be smaller compared to the others (although
in pymol all of them were identified using the same selection). So
probably this is an issue of PNG command, which I used to make a
screenshot.

Also one question: as it can be seed from my script I used command
split states for all_clusters object (which contain 100 conformations
of the centre of mass) and then operate with the visualization of
splited states. I noticed that the multi-model object is still exist
along with its separate models, which command could be used to disable
its visualization in GUI (like if I click on it in the context menu,
while operating in gui)?

Cheers,
J.

пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay :
>
> Hi Jeff,
>
> The sphere size is controlled by the vdw property, to change it:
> alter *, vdw=1.0 # this will set the sphere size to be equal for all atom 
i.e. hydrogens atom would be same size as carbon
>
> you also need to use the "rebuild" command to implement the changes
>
> At this point, you can control the sphere sizes consistently using:
> set sphere_scale, 1.5 # or what ever size you need
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and 
Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 26/2/21, 2:15 am, "Jeff Saxon"  wrote:
>
> Dear Pymol Users,
>
> Working on the visualisation of protein-ligand interactions, notably
> focusing on the visualisation of sphres atoms covered protein surface,
> I noticed on the resulted PNG that some sphere objects (located on the
> backing plane) looks VERY small compared to the rest. For example as
> it could be seen while major spheres represent like spheres, some of
> them look like dots, while in the pml session everything looks
> correctly. How could I fix using some pymol settings ?
> Thank you in advance!
> J
>



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Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

[Jeff Saxon]

Thank you very much, Ali!
Yes, actually, I suppose I have set up vdw radii using those commands,
considering specific selections,e.g this is part of my pymol script
that I am using in bash.
$pymol -c -d "
from pymol import cmd

cmd.load('${storage}/${syst_name}/all_clusters.pdb')
cmd.split_states('all_clusters*')
cmd.select('all_clusters*')
cmd.show('spheres', 'sele')
cmd.set('sphere_transparency', '0.2', 'sele')
cmd.color('marine', 'sele' )
cmd.alter('all_clusters*', 'vdw=0.75')
cmd.select('all_clusters*')
cmd.show( 'spheres', 'sele' )
cmd.rebuild()
cmd.bg_color('white')
cmd.save('${syst}/${syst_name}.pse')
cmd.png('${vizu}/${syst_name}.png',width=${image},height=${image},dpi=50,ray=0)
"

Eventually in my saved pml session everything looks fine BUT on the
png image some of the spheres (notably located on the back plane in
the space) are appeared to be smaller compared to the others (although
in pymol all of them were identified using the same selection). So
probably this is an issue of PNG command, which I used to make a
screenshot.

Also one question: as it can be seed from my script I used command
split states for all_clusters object (which contain 100 conformations
of the centre of mass) and then operate with the visualization of
splited states. I noticed that the multi-model object is still exist
along with its separate models, which command could be used to disable
its visualization in GUI (like if I click on it in the context menu,
while operating in gui)?

Cheers,
J.

пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay :
>
> Hi Jeff,
>
> The sphere size is controlled by the vdw property, to change it:
> alter *, vdw=1.0 # this will set the sphere size to be equal for all atom 
> i.e. hydrogens atom would be same size as carbon
>
> you also need to use the "rebuild" command to implement the changes
>
> At this point, you can control the sphere sizes consistently using:
> set sphere_scale, 1.5 # or what ever size you need
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
> On 26/2/21, 2:15 am, "Jeff Saxon"  wrote:
>
> Dear Pymol Users,
>
> Working on the visualisation of protein-ligand interactions, notably
> focusing on the visualisation of sphres atoms covered protein surface,
> I noticed on the resulted PNG that some sphere objects (located on the
> backing plane) looks VERY small compared to the rest. For example as
> it could be seen while major spheres represent like spheres, some of
> them look like dots, while in the pml session everything looks
> correctly. How could I fix using some pymol settings ?
> Thank you in advance!
> J
>


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[PyMOL] Question: Align object from group (and move rest of group with it)

[Jacek Kozuch]

Dear all,

I am trying to align (or pair fit) two structures and, at the same time,
move a density map belonging to the mobile structure with the alignment.
What would be the best way to achieve that?

I'd appreciate help or suggestions!

Thanks in advance!

Best,
Jacek






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Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

[Ali Saad Kusay]

Hi Jeff, 

The sphere size is controlled by the vdw property, to change it:
alter *, vdw=1.0 # this will set the sphere size to be equal for all atom i.e. 
hydrogens atom would be same size as carbon

you also need to use the "rebuild" command to implement the changes

At this point, you can control the sphere sizes consistently using:
set sphere_scale, 1.5 # or what ever size you need

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
 

On 26/2/21, 2:15 am, "Jeff Saxon"  wrote:

Dear Pymol Users,

Working on the visualisation of protein-ligand interactions, notably
focusing on the visualisation of sphres atoms covered protein surface,
I noticed on the resulted PNG that some sphere objects (located on the
backing plane) looks VERY small compared to the rest. For example as
it could be seen while major spheres represent like spheres, some of
them look like dots, while in the pml session everything looks
correctly. How could I fix using some pymol settings ?
Thank you in advance!
J


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[PyMOL] Question about python command in PyMOL

[Hrutvik Bhavsar]

Hello,

My name is Vik, I'm writing a python script that allows a user to input a
TSV (tab-separated value) file of PDB's which then edits them. I'm now
trying to change the code so that it can run directly in PyMOL instead of
having to run this python script and PyMOL separately. I'm having trouble
changing the python script so that it can run 100% in Pymol. I've pasted my
script below. Please let me know if there's a way to modify my code to
actually run in PyMOL. Thank you for your help.

Sincerely, Vik

import os

print("Files present with the .tsv extension:")
for file in os.listdir():
if file[-4:] == ".tsv":
print(file)

userinput = input('Enter the name of the TSV file you would like to be read:')
TSVfile = open(userinput)

#empty things filled later by script
unique = set()
f = open("ColorAndAlign.pml", "a")

#Eliminates duplicate PDBs
for row in TSVfile:
a = row.split()
if a[0] =="pdb":
continue
unique.add(a[0])
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[PyMOL] Question about multi-sequence edition in PyMOL

[sepehr dejdar]

Hi,

I have a question regarding adding peptide sequence to the original
sequence in PyMOL. I have an original structure of a nanoparticle
consisting of 420 monomers and I like to add a similar peptide sequence to
each monomer. Is that any easy way to apply a sequence addition/ change to
one monomer and apply it to the. whole structure rather than going and
adding the sequence manually 420 times in PyMOL?

Sincerely,
Sepehr
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Re: [PyMOL] Question about python commands in PyMOL

[Ali Kusay]

Hi Hrutvik,

The print function doesn’t actually execute the PyMOL commands the “cmd” module 
does

Change the prints to:
cmd.load(“1u8q.pdb”)
cmd.color(“red”,”chain y”)

For specific instruction on how to use the cmd based functions, visit the PyMOL 
wiki

Two other things:

  1.  the color function does not need to need to be extended as it is already 
built into PyMOL
  2.  PyMOL already has a load function which may be overwritten using your new 
load function, call it something else just to be safe

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
Email: akus8...@uni.sydney.edu.au

From: Ali Kusay 
Date: Thursday, 2 July 2020 at 8:55 pm
To: Ali Kusay 
Subject: FW: [PyMOL] Question about python commands in PyMOL



From: Hrutvik Bhavsar
Sent: Thursday, 2 July 2020 9:26:23 AM (UTC+10:00) Canberra, Melbourne, Sydney
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Question about python commands in PyMOL
Hello,

I'm writing a python script that loads in PDBs then selects certain chains 
colors them according to a standardized chart. However, I've run into the issue 
where my when I try running my script in Pymol via the run command it just 
displays the text on the python script but doesn't actually execute the 
command. I've pasted a sample script below. Please let me if there's a way to 
fix this. Thank you for your help.
Sincerely, Hrutvik.


from pymol import cmd, stored

def load( arg1):

print ("load 1u8q.pdb")
print ("color red, (chain y)" + "\n")

return (arg1)

cmd.extend( "load", load );
cmd.extend( "color", color );


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[PyMOL] Question about python commands in PyMOL

[Hrutvik Bhavsar]

Hello,

I'm writing a python script that loads in PDBs then selects certain chains
colors them according to a standardized chart. However, I've run into the
issue where my when I try running my script in Pymol via the run command it
just displays the text on the python script but doesn't actually execute
the command. I've pasted a sample script below. Please let me if there's a
way to fix this. Thank you for your help.
Sincerely, Hrutvik.

from pymol import cmd, stored

def load( arg1):

print ("load 1u8q.pdb")
print ("color red, (chain y)" + "\n")

return (arg1)

cmd.extend( "load", load );
cmd.extend( "color", color );
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[PyMOL] Question: How can I analyze the binding strength/energy between a small molecule and DNA using Pymol?

[Alexander Richardson]

Dear PyMOL maillist people:
I am new to mail lists. Please excuse any breaks of convention.
I suspect that a small molecule I am working with may have some DNA binding
property due to its triphenylphosphonium group. I would like to assess this
using Pymol. How could I do this? I do not have much background in
programming or how to use Pymol commands in general.
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Re: [PyMOL] Question about Pymol method / ESP rendering

[Taka Seri]

Hi Thomas,
Thank you for your reply.
I made the cube file by using psi4 which is one of quantum chemistry
package.
I will check the file.

Kind regards,
Taka

2019年6月11日(火) 19:40 Thomas Holder :

> Hi Taka,
>
> Your ESP.cube file doesn't look like an electrostatic potential map, it
> looks like electron density. You need two map files, one for the density,
> and one for the ESP.
>
> Cheers,
>   Thomas
>
> > On Jun 8, 2019, at 12:39 AM, Taka Seri  wrote:
> >
> > Dear Pymol users,
> > I am newbie of Pymol.
> > I have a question of coloring method. I would like to draw isosurface
> with ESP and would like to set color with ramp_new function.
> > Attached files are example.
> > When I load ESP file and type following command, I could get isosurface.
> > But I could get only blue colored surface after setting color with
> ramp_new function.
> >
> > > isosurface esp_surf, ESP, 0.2
> > > ramp_new color_map, ESP, [-0.1, 0.1]
> >
> > I read following url and it worked well.
> > https://pymolwiki.org/index.php/Ramp_New
> >
> > Is something wrong in my ESP file or approach? Any advice or suggestions
> will be greatly appreciated.
> >
> > Kind regards,
> >
> > Taka
> > ___
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> --
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> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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Re: [PyMOL] Question about Pymol method / ESP rendering

[Thomas Holder]

Hi Taka,

Your ESP.cube file doesn't look like an electrostatic potential map, it looks 
like electron density. You need two map files, one for the density, and one for 
the ESP.

Cheers,
  Thomas

> On Jun 8, 2019, at 12:39 AM, Taka Seri  wrote:
> 
> Dear Pymol users,
> I am newbie of Pymol.
> I have a question of coloring method. I would like to draw isosurface with 
> ESP and would like to set color with ramp_new function.
> Attached files are example.
> When I load ESP file and type following command, I could get isosurface.
> But I could get only blue colored surface after setting color with ramp_new 
> function.
> 
> > isosurface esp_surf, ESP, 0.2
> > ramp_new color_map, ESP, [-0.1, 0.1]
> 
> I read following url and it worked well.
> https://pymolwiki.org/index.php/Ramp_New
> 
> Is something wrong in my ESP file or approach? Any advice or suggestions will 
> be greatly appreciated.
> 
> Kind regards,
> 
> Taka
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--
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Schrödinger, Inc.



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[PyMOL] Question about polymer selection criteria

[Kung, Ryan]

Hello,

I have a question about how the pymol polymer.nucleic selection defines
what is nucleic? Is there a list of atom names that are required? Does it
have to actually be part of a polymer for the selection process to identify
it? If someone can help me understand this, that would be great.

Thank you,
Ryan Kung
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[PyMOL] Question about pymol movies

[Miguel Garavís]

Hi Pymol Users,

I need your help with an issue related to movie in pymol.
I know how to change the representation of the molecule that appears in my
movie at a given frame but I don't find the way to change the
representation of just a given part of such molecule, lets say make some
residues become partially transparent or change color while the rest keep
the same appearance.
I am following section "Motions and Representations" in this tutorial
https://pymolwiki.org/index.php/MovieSchool_5 but it doesn't work. Once I
change the representation of the chosen residues, they remain with the new
aspect along the whole movie...

Could somebody give me a clue on how to proceed?

Thank you very much in advance!

Kind regards,

Miguel
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Re: [PyMOL] PyMol Question

[Spencer Bliven]

Mohsen–

set transparency , .5, sele

Cheers,
Spencer

On Tue, Nov 3, 2015 at 3:18 AM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:

> Hi there,
>
>
>
> I was wondering how I can make the surface of a selected part of a protein
> transparent? I tried transparency command, but, I came up with a message
> that “transparency” was not found.
>
>
>
> Thank you
>
>
> --
>
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[PyMOL] PyMol Question

[Mohsen Chitsaz]

Hi there,

I was wondering how I can make the surface of a selected part of a protein 
transparent? I tried transparency command, but, I came up with a message that 
"transparency" was not found.

Thank you
--
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[PyMOL] Question regarding scene states

[Jordan Willis]

Hi List,

I figured out a hack way to fix my last question. That's ok, because I have 
another one. In my movie I have some objects with multiple states, and some 
objects with one. Is there a way to use mset (or in my case madd) for the 
multiple state objects and disregard the other objects?

For some reason mset and madd when working with multi-state objects using this 
command:

mset 1 -10 x10

is giving the multi-state objects ten frames but then appending the 
single-state objects an additional 10 frames. Does anyone know if this can be 
done? 

sorry to spam the list,

Jordan



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Re: [PyMOL] Question regarding scene states

[Jordan Willis]

Sorry,

I found the answer to my own question.

madd 1 -10 

If you don't use xframes, then it won't add additional frames to single-state 
objects. I can't quite figure out the rationale for that but if you already 
have pre-loaded states before you use mset, you can't request additional 
frames. However if I didn't want to map 1 state to 1 frame, this makes it 
impossible.

For instance

#show each state for 3 frames
madd 1 -30 x90

seems impossible now,

but close enough,
Jordan







On Nov 10, 2012, at 11:46 PM, Jordan Willis jwillis0...@gmail.com wrote:

 Hi List,
 
 I figured out a hack way to fix my last question. That's ok, because I have 
 another one. In my movie I have some objects with multiple states, and some 
 objects with one. Is there a way to use mset (or in my case madd) for the 
 multiple state objects and disregard the other objects?
 
 For some reason mset and madd when working with multi-state objects using 
 this command:
 
 mset 1 -10 x10
 
 is giving the multi-state objects ten frames but then appending the 
 single-state objects an additional 10 frames. Does anyone know if this can be 
 done? 
 
 sorry to spam the list,
 
 Jordan
 
 


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[PyMOL] question about biological units, states, etc.

[Bourgaize David]

Hello, all.

First let me announce that I am not a PyMOL poweruser, and I have virtually no 
experience with crystallography and its data files. I have been plugging along 
using the PyMOLwiki as my knowledge-base for years, but cannot seem to wrap my 
head around certain issues.

For example, 6pfk (phosphofructokinase) exists as a file that, when fetched, 
opens as a complete biological unit (a tetramer), with chains A, B, C, and D. 
However, 4pfk is only one subunit. When I then fetch 4pfk, type=pdb1 in order 
to obtain the biological unit, I can split_states and delete the original 4pfk. 
This leaves me with  a biological unit, but one in which each chain is its own 
object.

Ultimately, I would like to be able to align/superimpose various parts of these 
two structures. Is there an easy way to do this, given that one is a single 
object with multiple chains, and the other is four separate objects? Or. 
Alternatively, is there a way to convert the 4pfk biological unit into a single 
object, with chains A, B, C, and D?

Thanks-

Dave Bourgaize
Whittier College
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Re: [PyMOL] question

[Thomas Holder]

Hi Mona,

 I am very interested to here if it is possible to align a stick
 structure with a cartoon strucrture in Pymol?

structure alignment is independent of visual representation. So yes, you
can align a stick structure to a cartoon structure.

 Is it possible to put the short aa code or name in the peptide 
 structure in pymol?

you can add labels to atoms. So to label each residue with its name
(resn), just label all CA atoms:

PyMOL label name CA, resn


Cheers,
   Thomas

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Re: [PyMOL] question

[Jordan Willis]

Was my message received by the pymol group about combining camera and object 
motions at the same time? It said it was held for review. I have copy myself 
on the mailman server, but I never seem to receive my own posting.

Jordan


On Sep 19, 2012, at 5:35 AM, Thomas Holder wrote:

 Hi Mona,
 
 I am very interested to here if it is possible to align a stick
 structure with a cartoon strucrture in Pymol?
 
 structure alignment is independent of visual representation. So yes, you
 can align a stick structure to a cartoon structure.
 
 Is it possible to put the short aa code or name in the peptide 
 structure in pymol?
 
 you can add labels to atoms. So to label each residue with its name
 (resn), just label all CA atoms:
 
 PyMOL label name CA, resn
 
 
 Cheers,
   Thomas
 
 -- 
 Thomas Holder
 MPI for Developmental Biology
 Spemannstr. 35
 D-72076 Tübingen
 
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Re: [PyMOL] Question about mutagenesis wizard

[Troels Emtekær Linnet]

Hi.

I tried a little:

*test1.pml*
# See http://www.pymolwiki.org/index.php/Peptide_Sequence
# See http://www.pymolwiki.org/index.php/propka

reinitialize
cd C:\Users\tlinnet\Desktop

python
for aa in CVGLTSW:
cmd._alt(string.lower(aa))
python end
create pdb1, cys
remove cys
delete cys
save pdb1.fasta, pdb1

###First time
#python
#for aa in ALTWSIK:
#cmd._alt(string.lower(aa))
#python end
#create pdb2, ala
#remove ala
#delete ala
#translate [-6,-15,0], pdb2
#save pdb2.pdb, pdb2
### Second time
load pdb2.pdb

alter pdb1, chain='A'
alter pdb2, chain='A'
rebuild
create pdb3, pdb1

chainresnresi3 = []
chainresnresi2 = []
iterate pdb3 and name CA, chainresnresi3.append([pdb3,chain,resn,resi])
iterate pdb2 and name CA, chainresnresi2.append([pdb2,chain,resn,resi])
#print chainresnresi3
#print chainresnresi2

python
cmd.wizard(mutagenesis)
for i in range(len(chainresnresi2)):
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(%s%chainresnresi2[i][2])
#print %s%chainresnresi2[i][2]

selection=/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
#print
/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)

translate [10,-25,0], pdb3

*test2.pml*
reinitialize
cd C:\Users\tlinnet\Desktop

fab CVGLTSW, pdb1, resi=1, chain=A
save pdb1.fasta, pdb1

fab ALTWSIK, pdb2, resi=1, chain=A
translate [0,-15,0], pdb2

create pdb3, pdb1
translate [0,-30,0], pdb3

chainresnresi3 = []
chainresnresi2 = []
iterate pdb3 and name CA, chainresnresi3.append([pdb3,chain,resn,resi])
iterate pdb2 and name CA, chainresnresi2.append([pdb2,chain,resn,resi])
print chainresnresi3
print chainresnresi2

python
cmd.wizard(mutagenesis)
for i in range(len(chainresnresi2)):
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(%s%chainresnresi2[i][2])
#print %s%chainresnresi2[i][2]

selection=/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
#print
/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)

*test3.pml*
reinitialize
cd C:\Users\tlinnet\Desktop

load pdb1.fasta
load pdb2.fasta
translate [0,-15,0], pdb2

create pdb3, pdb1
translate [0,-30,0], pdb3

chainresnresi3 = []
chainresnresi2 = []
iterate pdb3 and name CA, chainresnresi3.append([pdb3,chain,resn,resi])
iterate pdb2 and name CA, chainresnresi2.append([pdb2,chain,resn,resi])
print chainresnresi3
print chainresnresi2

python
cmd.wizard(mutagenesis)
for i in range(len(chainresnresi2)):
cmd.do(refresh_wizard)
cmd.get_wizard().set_mode(%s%chainresnresi2[i][2])
#print %s%chainresnresi2[i][2]

selection=/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
#print
/%s//%s/%s%(chainresnresi3[i][0],chainresnresi3[i][1],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)

*pdb1.fasta*
pdb1
CVGLTSW

*pdb2.fasta*
pdb2
ALTWSIK

Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234



2012/9/14 Maurício Menegatti Rigo mauriciomr1...@gmail.com

 Hi Thomas,

 thank you for your response. Actually,  the  modeling part comes later in
 the process. First, I need  to perform  this step  in pymol. In fact, it
 would facilitate the modeling process.

 Sincerely,
 --
 Maurício M Rigo


 2012/9/14 Thomas Holder spel...@users.sourceforge.net

 Hi Maurício,

 what you describe here is called homology modeling. Although PyMOL has
 some modeling capabilities, I'd strongly recommend to use a real homology
 modeling tool such as MODELLER to do this.

 http://salilab.org/modeller/

 Hope that helps.

 Cheers,
   Thomas

 Maurício Menegatti Rigo wrote, On 09/14/12 19:44:

 Dear Pymol users,

 I'm  a begginer  with command lines in Pymol.  I'm trying to
 complete  the following task through a pymol  script:

 1) Write a file named file1.txt with an aminoacid sequence (e.g.
 CVGLTUW)

 2) Open  a .pdb molecule (file2.pdb) with the same number of
 residues, but with a different sequence (e.g. ALTWSIK)

 3) Write a code where the pymol will pick each residue of the
 file2.pdb (I believe that this could be made by the mutagenesis
 wizard command) and mutate for the respective aminoacid written in
 my file1.txt

 4) Save the new filein .pdb format (file3.pdb)

 I'll be very greatful for any help!

 Thanks  in advance,
 -- M.Sc. Maurício Menegatti Rigo
 Núcleo de Bioinformática do Laboratório de Imunogenética
 Departamento de Genética
 Instituto de Biociências
 Universidade Federal do Rio Grande do Sul - Campus do Vale
 Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M
 CEP:91501-970 Caixa Postal 15053
   

Re: [PyMOL] Question about mutagenesis wizard

[Thomas Holder]

Hi Maurício,

what you describe here is called homology modeling. Although PyMOL has 
some modeling capabilities, I'd strongly recommend to use a real 
homology modeling tool such as MODELLER to do this.

http://salilab.org/modeller/

Hope that helps.

Cheers,
   Thomas

Maurício Menegatti Rigo wrote, On 09/14/12 19:44:
 Dear Pymol users,
 
 I'm  a begginer  with command lines in Pymol.  I'm trying to
 complete  the following task through a pymol  script:
 
 1) Write a file named file1.txt with an aminoacid sequence (e.g.
 CVGLTUW)
 
 2) Open  a .pdb molecule (file2.pdb) with the same number of
 residues, but with a different sequence (e.g. ALTWSIK)
 
 3) Write a code where the pymol will pick each residue of the
 file2.pdb (I believe that this could be made by the mutagenesis
 wizard command) and mutate for the respective aminoacid written in
 my file1.txt
 
 4) Save the new filein .pdb format (file3.pdb)
 
 I'll be very greatful for any help!
 
 Thanks  in advance,
 -- 
 M.Sc. Maurício Menegatti Rigo
 Núcleo de Bioinformática do Laboratório de Imunogenética
 Departamento de Genética
 Instituto de Biociências
 Universidade Federal do Rio Grande do Sul - Campus do Vale
 Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M
 CEP:91501-970 Caixa Postal 15053
 Porto Alegre, RS, Brasil
 Tel: +55 51 3308 9938 tel:%2B55%2051%203308%209938

-- 
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MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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[PyMOL] Question about ray tracing, set_view, surface smoothness

[Gudrun Lotze]

Dear all,

I wish to ray trace my object so it looks nice. I have chosen a mesh as surface 
representation.

I did 
viewport 1024, 768
ray 1024, 768

But the mesh is black afterwards and not anymore blue.
Is there a chance to keep the color and have less dominant lines for the mesh?

Is there a chance to view the object in question for example in the XY, YZ 
plane? Are there somewhere easy rotation matrix available?
I tried to bring my object manually into the YZ plane view, for example, but it 
works only halfhearted. 
It would be nice to be able to tell pymol in a very easy way which view I would 
like to see the object.

Thank you for your patience.
Kind regards
Gudrun

 
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Re: [PyMOL] Question about ray tracing, set_view, surface smoothness

[Pete Meyer]

Hi Gudrun,

 But the mesh is black afterwards and not anymore blue.

You may want to check your light position, or try a slighter blue.

 Is there a chance to keep the color and have less dominant lines for the mesh?

I'm not artistically skilled enough to know about less dominant lines, 
but the mesh_width setting can be used to make thinner (or thicker) lines.

 Is there a chance to view the object in question for example in the XY, YZ 
 plane? Are there somewhere easy rotation matrix available?
 I tried to bring my object manually into the YZ plane view, for example, but 
 it works only halfhearted. 
 It would be nice to be able to tell pymol in a very easy way which view I 
 would like to see the object.

The turn/rotate commands can be used fairly easily for 90 degree turns; 
but I'm not sure if that's what you're asking about.

Pete


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[PyMOL] Question

[Bachar Cheaib]

Dear All,

I am a Pymol's user

I would like to know how could I find the algorithm publication of three
functions for superimposition of multi-structures?

1- fit
2- align
3- super

I would thanks in advance for your reply

Sincerely



B. Ch

On Wed, Feb 15, 2012 at 12:20 PM, Bachar Cheaib cheaib.bac...@gmail.comwrote:

 Dear All,

 I am a Pymol's user

 I would like to know how could I find the algorithm publication of three
 functions for superimposition of multi-structures?

 1- fit
 2- align
 3- super

 I would thanks in advance for your reply

 Sincerely



 BaCh


 On Wed, Feb 15, 2012 at 11:31 AM, 
 pymol-users-requ...@lists.sourceforge.net wrote:

 Send PyMOL-users mailing list submissions to
pymol-users@lists.sourceforge.net

 To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/pymol-users
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 When replying, please edit your Subject line so it is more specific
 than Re: Contents of PyMOL-users digest...


 Today's Topics:

   1. Re: Open Source PyMOL v1.5.0.1 (David Hall)
   2. Re: solid objects (Jason Vertrees)
   3. compiling Open Source PyMOL v1.5.0.1 (Thomas Stout)
   4. 1.5 version runs slow with large objects (Vitali Stanevich)
   5. Re: Open Source PyMOL v1.5.0.1 (?? ??)


 --

 Message: 1
 Date: Tue, 14 Feb 2012 12:03:33 -0500
 From: David Hall li...@cowsandmilk.net
 Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1
 To: Jason Vertrees jason.vertr...@schrodinger.com
 Cc: pymol-users@lists.sourceforge.net
 Message-ID:

 capuwn_9wwuwpcaa6htud3vsmbxmwguynqnj-kzdwowdt7b_...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees
 jason.vertr...@schrodinger.com wrote:
  Greetings,
 
  It is my pleasure to announce the release of open source PyMOL
  v1.5.0.1. The source code has been committed to the open-source
  repository. It is revision 3976. An svn tag and downloadable bz2
  source file were also created. All of this is accessible form the
  PyMOL project page on SourceForge
  (http://sourceforge.net/projects/pymol/).

 For those of you on openSUSE, I've updated the pymol packages in the
 openSUSE Build Service to this release. You can test this new version
 by visiting
 http://software.opensuse.org/download.html?project=devel:languages:pythonpackage=pymol
 and choosing the appropriate openSUSE release and architecture.

 -David



 --

 Message: 2
 Date: Tue, 14 Feb 2012 12:40:02 -0500
 From: Jason Vertrees jason.vertr...@schrodinger.com
 Subject: Re: [PyMOL] solid objects
 To: Daniel Larsson lars...@xray.bmc.uu.se
 Cc: pymol-users@lists.sourceforge.net
 Message-ID:

 caax+4zfqqdafwyiqmmdm3hkuiyrtvhoin70bc5eof4hbeae...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Daniel,

 Filling clipped spheres is not yet available. We'll look at adding it.

 Cheers,

 -- Jason

 On Tue, Feb 14, 2012 at 12:00 PM, Daniel Larsson lars...@xray.bmc.uu.se
 wrote:
  Thanks for the quick reply.
 
  A closely related issue is that clipped spheres are rendered very
 strangely. It seems they only consists of a half-sphere and if the clipping
 plane intersects the sphere in the front-most half, then you can see
 straight through it.
 
  Daniel
 
 
  On Feb 14, 2012, at 17:50 , Jason Vertrees wrote:
 
  Daniel,
 
  # reset the setting
 
  set ray_interior_color, default
 
  # set the setting for each object
 
  set ray_interior_color, marine, protA
 
  set ray_interior_color, magenta, protB
 
 
  PyMOL does not support this via the 'draw' command (unless you set
  draw_mode, 3, but that's just ray tracing). Please file an RFE and
  we'll look into it.
 
  Cheers,
 
  -- Jason
 
  On Tue, Feb 14, 2012 at 11:17 AM, Daniel Larsson 
 lars...@xray.bmc.uu.se wrote:
  Hi,
 
  Is there a way to render truncated/clipped objects as dense. I.e. a
 lid on clipped objects, such as surfaces or spheres.
 
  Want I want is something similar to the A sliced image example in
 the wiki gallery (http://www.pymolwiki.org/index.php/Gallery), but with
 that technique I can only pick one color for all molecules. I would like to
 set ray_interior_color different for different molecules or objects.
 Basically, I want the color to be the same on the inside as on the outside.
 It would be great if it would work with the draw command as well.
 
  Is it possible with version 1.5? Or is there a chances of having this
 implemented anytime soon?
 
  Daniel
 
 
 
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[PyMOL] Question Iterate

[Martin Hediger]

In this example below (from Thomas), the method 'iterate' is used. The 
function saves every amino acid of a structure to a separate file. First 
of all, I'm not sure of how to understand the docs:

 iterate iterates over an expression within a temporary namespace for 
each atom.

What does temporary namespace for each atom mean? Also, since 'iterate' 
is used within the while-loop, are we only iterating over the single 
amino acid? Its confusing me because I constantly think of iterate as 
somekind of short hand notation of a for-loop, but I guess thats not it. 
It would be great if somebody could explain the iterate function a bit 
more to me.

Thanks for your feedback.
Martin

# *
# import statements
def seq(state, selection=name ca or resn hoh or resn lig):
  cmd.select(prot, selection)
  while cmd.pop(_tmp, prot):
  cmd.iterate(_tmp, stored.x=(resn,resv))
  # Special case 1: Waters.
  if stored.x[0] == 'HOH':
  filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
  # Special case 2: Substrate.
  elif stored.x[0] == 'LIG':
  filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
  # Other: protein back-bone.
  else:
  filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(), 
stored.x[1], state)
  cmd.save(filename, byres _tmp)
  cmd.delete('_tmp prot')

cmd.extend('seq', seq)
# -



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Re: [PyMOL] Question Iterate

[Tsjerk Wassenaar]

Hi Martin,

The temporary namespace for an atom means that variables like 'resn'
can be used to refer to the attribute with that name on the atom
instance.

You are right that iterate is here used to iterate over a single atom.
That does seem a bit odd :p But it seems to be a more straightforward
way to get to the properties desired.

This is what I would do:

residues=set()
iterate all, residues.add((chain,resn,resi))
for res in residues: cmd.save(%s-%s-%s.pdb%res,chain %s and resn %s
and resi %s%res)

Of course that could be easily forged into a nice function :)

Hope it helps,

Tsjerk
On Mon, Nov 28, 2011 at 3:57 PM, Martin Hediger ma@bluewin.ch wrote:
 In this example below (from Thomas), the method 'iterate' is used. The
 function saves every amino acid of a structure to a separate file. First
 of all, I'm not sure of how to understand the docs:

  iterate iterates over an expression within a temporary namespace for
 each atom.

 What does temporary namespace for each atom mean? Also, since 'iterate'
 is used within the while-loop, are we only iterating over the single
 amino acid? Its confusing me because I constantly think of iterate as
 somekind of short hand notation of a for-loop, but I guess thats not it.
 It would be great if somebody could explain the iterate function a bit
 more to me.

 Thanks for your feedback.
 Martin

 # *
 # import statements
 def seq(state, selection=name ca or resn hoh or resn lig):
      cmd.select(prot, selection)
      while cmd.pop(_tmp, prot):
          cmd.iterate(_tmp, stored.x=(resn,resv))
          # Special case 1: Waters.
          if stored.x[0] == 'HOH':
              filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
          # Special case 2: Substrate.
          elif stored.x[0] == 'LIG':
              filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
          # Other: protein back-bone.
          else:
              filename = 'seq-%s%d-%s.pdb' % (one_letter[stored.x[0]].lower(), 
 stored.x[1], state)
          cmd.save(filename, byres _tmp)
      cmd.delete('_tmp prot')

 cmd.extend('seq', seq)
 # -



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* Zernike Institute for Advanced Materials
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The Netherlands

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Re: [PyMOL] Question about the .obj file saved by Pymol

[Jason Vertrees]

Hi Francois,

Woops--sorry for the delay.  I think only the outside vertices are
sent.  To get the inside, try

set surface_cavity_mode, 2

before surfacing and exporting.  You can also set that to '3' to
include pockets as well as cavities.

Cheers,

-- Jason

On Wed, Mar 2, 2011 at 3:04 AM, Francois Berenger beren...@riken.jp wrote:
 Hello,

 If I use save myscene.obj and I was looking at the surface
 representation of a molecule, does the file contains only the external
 surface of the protein, or are the internal cavities also included?

 Thanks,
 F.

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[PyMOL] Question about the .obj file saved by Pymol

[Francois Berenger]

Hello,

If I use save myscene.obj and I was looking at the surface 
representation of a molecule, does the file contains only the external 
surface of the protein, or are the internal cavities also included?

Thanks,
F.

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[PyMOL] Question about the .obj file saved by Pymol

[Francois Berenger]

Hello,

If I use save myscene.obj and I was looking at the surface 
representation of a molecule, does the file contains only the external 
surface of the protein, or are the internal cavities also included?

Thanks,
F.

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[PyMOL] Question about Iterate and Edit-Mode

[Martin Hediger]

Dear All
I am trying to get behind the way 'iterate' works, since I see it quite 
frequently in PyMOL scripts.
The example in the help page is a bit limited in the sense that I cant 
explain to myself what actually is happening.

Say, if I were to write the functionality of 'iterate' using a for-loop, 
how would this for-loop look like?
Something like this maybe?

for i in selection:
 i.expression()

I'm a bit confused about what can go into 'expression'.

The second question is related to the Edit-Mode of PyMOL. When I switch 
to Edit-Mode and click on a atom, a couple of states/objects (?) appear 
in the object list: pk1, pkmol, pkresi, pkchain, pkobject.
What do these objects mean? What are they useful for? I'm sure there is 
a reason for them, but I cant figure it out.

Thanks a lot for your help guys.

Martin

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Re: [PyMOL] Question on how to identify residue number on protein surface

[Jason Vertrees]

Hi Jay Song,

Why not use code that's already available?  Check out
http://pymolwiki.org/index.php/FindSurfaceResidues.

Cheers,

-- Jason

2010/7/12 SongJianHui gigi...@hotmail.com:
 Hi all,

 I am trying using PyMol to identify the residue numbers on a protein
 surface. I have been thinking use a low efficient way to do this, i.e.,
 color each residues in surface display mode. I wonder if there is a better
 way to fulfill this mission.

 Thanks in advance,

 Jay Song

 
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Re: [PyMOL] Question about ray

[Joel Tyndall]

Try setting your Pymol viewer to square dimensions first:

Viewport 600,600

Then try the ray command

This should work

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
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-Original Message-
From: Gudrun Lotze [mailto:gudrun.lo...@gmx.net] 
Sent: Wednesday, 23 June 2010 12:30 p.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Question about ray

Dear Pymol-Users,

I tried to ray my protein to get a good looking picture. I tried set  
ray_trace_mode, 0 and ray 1200, 1200. I always go a square around my  
protein and parts where not visible.
How can I get rid of that black border line and how can I ray my  
protein so it is on the whole page visible and not in a box cut off.
Thank you and kind regards
Gudrun Lotze


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Re: [PyMOL] Question about ray

[Jason Vertrees]

Hi all,

Joel's correct: to get the ray traced image to match the viewport, you
must set the viewport to the same aspect ratio as the output image:

# setup the viewport
viewport 800, 600

# zoom on the visible
zoom visible

# ray the scene
ray 800,600

# scale it up
ray 1600, 1200

Cheers,

-- Jason


On Tue, Jun 22, 2010 at 9:32 PM, Joel Tyndall joel.tynd...@otago.ac.nz wrote:
 Try setting your Pymol viewer to square dimensions first:

 Viewport 600,600

 Then try the ray command

 This should work

 Joel

 _
 Joel Tyndall, PhD

 Senior Lecturer in Medicinal Chemistry
 National School of Pharmacy
 University of Otago
 PO Box 56 Dunedin 9054
 New Zealand
 Skype: jtyndall
 http://www.researcherid.com/rid/C-2803-2008
 Pukeka Matua
 Te Kura Taiwhanga Putaiao
 Te Whare Wananga o Otago
 Pouaka Poutapeta 56 Otepoti 9054
 Aotearoa

 Ph / Waea   +64 3 4797293
 Fax / Waeawhakaahua +64 3 4797034


 -Original Message-
 From: Gudrun Lotze [mailto:gudrun.lo...@gmx.net]
 Sent: Wednesday, 23 June 2010 12:30 p.m.
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Question about ray

 Dear Pymol-Users,

 I tried to ray my protein to get a good looking picture. I tried set
 ray_trace_mode, 0 and ray 1200, 1200. I always go a square around my
 protein and parts where not visible.
 How can I get rid of that black border line and how can I ray my
 protein so it is on the whole page visible and not in a box cut off.
 Thank you and kind regards
 Gudrun Lotze


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[PyMOL] Thank you for answering my pymol question! -one more question

[JiangJiang Liu]

Dear Tsherk :
Thank you so much for your reply on my pymol question. Your suggestions are 
helpful to solve the question that has been confused me for so long.
I still have another related question. After I created the dimmer 
structure, do you know how to save the new structure as a pdb file? This 
created pdb file can be opened by the Microsoft word and have roughly twice the 
amount atom coordinates than the monomer pdb file.
Once again thank you for your kindly help!
Sincerely 
Jenna  
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Re: [PyMOL] Thank you for answering my pymol question! -one more question

[Tsjerk Wassenaar]

Hi Jenna,

I think you already managed (using 'save'). And of course there are
two times as many coordinates in a dimer, so the saved file will be
twice the size. By the way, before saving, you might want to make sure
the chains get different chain IDs, so you can easily address them
later:

alter original,chain=A
alter copied,chain=B
save dimer.pdb

Cheers,

Tsjerk

On Wed, Apr 7, 2010 at 1:34 AM, JiangJiang Liu jli...@uwo.ca wrote:
 Dear Tsherk :
     Thank you so much for your reply on my pymol question. Your suggestions
 are helpful to solve the question that has been confused me for so long.
     I still have another related question. After I created the dimmer
 structure, do you know how to save the new structure as a pdb file? This
 created pdb file can be opened by the Microsoft word and have roughly twice
 the amount atom coordinates than the monomer pdb file.
     Once again thank you for your kindly help!
 Sincerely
 Jenna



-- 
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post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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Re: [PyMOL] Question about measuring volume

[Xavier]

Hi Sing,

You have a few options.

You can try CASTp (either the web service or the PyMOL plugin). I think the 
.pocinfo file contains information about volumes.

You could also use Voidoo (http://xray.bmc.uu.se/usf/voidoo_man.html). In the 
distribution, there is a script (cavity.csh) can be used to used to run voidoo 
to find cavities. The resulting log files have information about volumes. To 
visualize the cavities, the resulting .ezd files have to bee converted to .ccp4 
with mapman.

Hope this helps,

Xavier

Xavier Deupi
Laboratory of Computational Medicine
Biostatistics Unit. School of Medicine
Universitat Autonoma de Barcelona
Bellaterra, 08193 (Barcelona)
Catalunya, EU
lmc.uab.cat

On Dec 17, 2009, at 8:16 AM, Kin Sing Stephen Lee wrote:

 Dear all,
 
 I am wondering if it is possible for me to measure the volume of the  
 binding pocket or the molecule in pymol? If no, any recommend program  
 for Mac for such purposes?
 
 Thank you very much
 
 Sing






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[PyMOL] Question about measuring volume

[Kin Sing Stephen Lee]

Dear all,

I am wondering if it is possible for me to measure the volume of the  
binding pocket or the molecule in pymol? If no, any recommend program  
for Mac for such purposes?

Thank you very much

Sing

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Re: [PyMOL] pymol question

[Tsjerk Wassenaar]

Hi,

You can draw a CGO circle in the yz plane using:

x1,y1,z1 = -0.1, 0, 0 # start point
r1,g1,b1 = 1,0,0 # color (red)
x2,y2,z2 = 0.1, 0, 0 # end point
r2,g2,b2 = 1,1,0 # color (yellow)
radius = 10
cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2,
g2, b2 ], cylinder1 )

To make it transparent, change it to

cmd.load_cgo( [ 25.0, 0.25, 9.0, x1, y1, z1, x2, y2, z2, radius, r1,
g1, b1, r2, g2, b2 ], cylinder1 )

The 9.0 stands for CYLINDER, but you'd need to 'from pymol.cgo import
*' to be able to use the keywords. Likewise, 25.0 stands for ALPHA,
controlling the transparency. Note that the cylinder may not look
quite round. It will do when you raytrace it. I couldn't find a
setting for cgo display quality...

Anyway, it may be that Micheals suggestion is better, but since the
question was for a cylinder... And with a bit of Python scripting such
a circle could be drawn with a given center and normal axis.

Hope it helps,

Tsjerk

On Tue, Jul 7, 2009 at 12:54 AM, Michael
Lernermglerner+sourcefo...@gmail.com wrote:
 I'm sure there's a way to actually draw a circle, but for your particular
 use it might be better to use a sphere. If you're comfortable with python
 scripting, you can use CGO objects. If not, you might do something like
 this:

 fetch 1hhp
 create thing, resi 24 and name ca # create a new object from some single
 atom selection
 alter thing, vdw=10.0 # set desired radius
 rebuild # necessary if spheres have already been shown
 show spheres, thing
 alter_state 1, thing, x,y,z = 50,60,10 # set desired x,y,z coords
 set sphere_transparency, 0.5, thing # make it transparent
 zoom
 ray

 you can also use something like select + within to select all residues
 within a cutoff, but I got the impression you wanted a nice visualization.


 Hope that helps,

 -michael

 On Mon, Jul 6, 2009 at 5:01 PM, Benjamin Michael Owen owe...@marshall.edu
 wrote:

 Does anyone know how to draw a circle with a given radius in pymol? I have
 a distance that I want to use to see what residues lie on the end of that
 radius, but I have no idea how to write the command to draw the circle.
 Could someone help me please?


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[PyMOL] pymol question

[Benjamin Michael Owen]

Does anyone know how to draw a circle with a given radius in pymol? I have a distance that I want to use to see what residues lie on the end of that radius, but I have no idea how to write the command to draw the circle. Could someone help me please?

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Re: [PyMOL] pymol question

[Michael Lerner]

I'm sure there's a way to actually draw a circle, but for your particular
use it might be better to use a sphere. If you're comfortable with python
scripting, you can use CGO objects. If not, you might do something like
this:

fetch 1hhp
create thing, resi 24 and name ca # create a new object from some single
atom selection
alter thing, vdw=10.0 # set desired radius
rebuild # necessary if spheres have already been shown
show spheres, thing
alter_state 1, thing, x,y,z = 50,60,10 # set desired x,y,z coords
set sphere_transparency, 0.5, thing # make it transparent
zoom
ray

you can also use something like select + within to select all residues
within a cutoff, but I got the impression you wanted a nice visualization.


Hope that helps,

-michael

On Mon, Jul 6, 2009 at 5:01 PM, Benjamin Michael Owen
owe...@marshall.eduwrote:

 Does anyone know how to draw a circle with a given radius in pymol? I have
 a distance that I want to use to see what residues lie on the end of that
 radius, but I have no idea how to write the command to draw the circle.
 Could someone help me please?


 --

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Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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Re: [PyMOL] Question about Pymol movie

[Warren DeLano]

Liyang,

This will only be of use to you if you happen to be a PyMOL subscriber,
but there is an example movie script somewhat like this in the official
online documentation:

http://delsci.info/dsc/dokuwiki/doku.php?id=example:animation:granzyme_h
ydrolysis

Cheers,
Warren

 -Original Message-
 From: liyang [mailto:liy...@moon.ibp.ac.cn] 
 Sent: Monday, March 02, 2009 9:49 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Question about Pymol movie
 
 Dear all,
I got two small molecule binded protein structures, during 
 the reaction, this molecule moves from one site to another. 
 Given the two pdb files, can I make a movie to simulate the 
 whole process in Pymol? Any suggestion will be appreciated.
 
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[PyMOL] Question about Pymol movie

[liyang]

Dear all,
   I got two small molecule binded protein structures, during the 
reaction, this molecule moves from one site to another. Given the
two pdb files, can I make a movie to simulate the whole process 
in Pymol? Any suggestion will be appreciated.

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Re: [PyMOL] another odd PyMOL question....

[DeLano Scientific]

Tom,

label all, color

will display the numeric color identifiers which can be used in place of
color names.  You can also use iterate to fetch them back out as a list:

stored.list = []
iterate all, stored.list.append(color)
print stored.list

Cheers,
Warren

--
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Subscriber Support Services
mailto:supp...@delsci.com


-Original Message-
From: Thomas Stout [mailto:tst...@exelixis.com] 
Sent: Tuesday, November 11, 2008 3:35 PM
To: pymol-users@lists.sourceforge.net; matthew.frank...@imclone.com
Subject: Re: [PyMOL] another odd PyMOL question


So, a follow up question becomes: is there a way to report what color
something is?

:)

-Tom 

-Original Message-
From: matthew.frank...@imclone.com [mailto:matthew.frank...@imclone.com]

Sent: Tuesday, November 11, 2008 1:52 PM
To: Thomas Stout
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] another odd PyMOL question



Thomas Stout tst...@exelixis.com wrote on 11/11/2008 04:46:38 PM:


 Hi again everyone --

 I have another odd PyMOL question: does anyone know if it is possible 
 to make selections based on what color certain atoms are?
 I need to do some wholesale re-coloring of a series of complicated 
 figures and it would be extremely useful if I could just say something
like:

 color  red, (everything that is currently blue)

 Thanks,
 Tom



How about:

 color red, yourmolecule and (color blue)

Works for me.  Of course, you have to know the color name for the color
you're looking at - maybe there's a way of getting the RGB values for an
atom?

- Matt

--
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Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


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Re: [PyMOL] another odd PyMOL question....

[Thomas Stout]

Ah!  spectacular

Thanks very much -- those two suggestions have just very likely saved me
HOURS of work!

-Tom 

-Original Message-
From: DeLano Scientific [mailto:del...@delsci.info] 
Sent: Tuesday, November 11, 2008 6:15 PM
To: Thomas Stout
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] another odd PyMOL question

Tom,

label all, color

will display the numeric color identifiers which can be used in place of
color names.  You can also use iterate to fetch them back out as a
list:

stored.list = []
iterate all, stored.list.append(color)
print stored.list

Cheers,
Warren

--
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Subscriber Support Services
mailto:supp...@delsci.com


-Original Message-
From: Thomas Stout [mailto:tst...@exelixis.com]
Sent: Tuesday, November 11, 2008 3:35 PM
To: pymol-users@lists.sourceforge.net; matthew.frank...@imclone.com
Subject: Re: [PyMOL] another odd PyMOL question


So, a follow up question becomes: is there a way to report what color
something is?

:)

-Tom 

-Original Message-
From: matthew.frank...@imclone.com [mailto:matthew.frank...@imclone.com]

Sent: Tuesday, November 11, 2008 1:52 PM
To: Thomas Stout
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] another odd PyMOL question



Thomas Stout tst...@exelixis.com wrote on 11/11/2008 04:46:38 PM:


 Hi again everyone --

 I have another odd PyMOL question: does anyone know if it is possible 
 to make selections based on what color certain atoms are?
 I need to do some wholesale re-coloring of a series of complicated 
 figures and it would be extremely useful if I could just say something
like:

 color  red, (everything that is currently blue)

 Thanks,
 Tom



How about:

 color red, yourmolecule and (color blue)

Works for me.  Of course, you have to know the color name for the color
you're looking at - maybe there's a way of getting the RGB values for an
atom?

- Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
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e-mail
is not the intended recipient, or the employee or agent responsible for
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[PyMOL] another odd PyMOL question....

[Thomas Stout]

 
Hi again everyone --
 
I have another odd PyMOL question: does anyone know if it is possible to
make selections based on what color certain atoms are?   I need to do
some wholesale re-coloring of a series of complicated figures and it
would be extremely useful if I could just say something like:
 
color  red, (everything that is currently blue)
 
Thanks,
Tom
 
PS - No, the original selections that were made to construct the figures
were not retained in the session file, just the completed scenes 


This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.


Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

Re: [PyMOL] another odd PyMOL question....

[Matthew . Franklin]

Thomas Stout tst...@exelixis.com wrote on 11/11/2008 04:46:38 PM:


 Hi again everyone --

 I have another odd PyMOL question: does anyone know if it is
 possible to make selections based on what color certain atoms are?
 I need to do some wholesale re-coloring of a series of complicated
 figures and it would be extremely useful if I could just say something
like:

 color  red, (everything that is currently blue)

 Thanks,
 Tom



How about:

 color red, yourmolecule and (color blue)

Works for me.  Of course, you have to know the color name for the color
you're looking at - maybe there's a way of getting the RGB values for an
atom?

- Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.

Re: [PyMOL] another odd PyMOL question....

[Thomas Stout]

So, a follow up question becomes: is there a way to report what color
something is?

:)

-Tom 

-Original Message-
From: matthew.frank...@imclone.com [mailto:matthew.frank...@imclone.com]

Sent: Tuesday, November 11, 2008 1:52 PM
To: Thomas Stout
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] another odd PyMOL question



Thomas Stout tst...@exelixis.com wrote on 11/11/2008 04:46:38 PM:


 Hi again everyone --

 I have another odd PyMOL question: does anyone know if it is possible 
 to make selections based on what color certain atoms are?
 I need to do some wholesale re-coloring of a series of complicated 
 figures and it would be extremely useful if I could just say something
like:

 color  red, (everything that is currently blue)

 Thanks,
 Tom



How about:

 color red, yourmolecule and (color blue)

Works for me.  Of course, you have to know the color name for the color
you're looking at - maybe there's a way of getting the RGB values for an
atom?

- Matt

--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this
e-mail is not the intended recipient, or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that reading it is strictly prohibited.  If you have received
this e-mail in error, please immediately return it to the sender and
delete it from your system.  Thank you.


This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.


Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

Re: [PyMOL] question about checking the performance of PyMOL

[Joonghyun Ryu]

Dear Warren

Thank you for your information.
It works fine.

Joonghyun
-Original Message-
From: DeLano Scientific [mailto:del...@delsci.info] 
Sent: Sunday, October 26, 2008 3:25 AM
To: 'Joonghyun Ryu'; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] question about checking the performance of PyMOL

 
Joonghyun,

To optimize performance and responsiveness, PyMOL tends to defer
compute-intensive tasks until their results are actually needed.  Thus,

cmd.show(surface)

Doesn't actually show a surface, it only sets the surface visibility flag on
the atoms present (for future reference).  An actual surface won't be
computed until PyMOL is asked to refresh or render the display.  When
running a script, you can force an update by calling:

cmd.refresh()

After cmd.show.

Cheers,
Warren



--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com


-Original Message-
From: Joonghyun Ryu [mailto:jh...@voronoi.hanyang.ac.kr] 
Sent: Friday, October 24, 2008 10:39 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] question about checking the performance of PyMOL

Hi, all

I am sending this email for asking you about checking the performance of
PyMOL.
I tried to check the elapsed time for the computation of a molecular surface
as follows.

--
import os
import cmd
import pymol

cmd.set(surface_quality, 2)

start = time.time()
cmd.show(surface)
end = time.time()
elapsedTime = (end - start)
print Elapsed time: , elapsedTime, sec.

--

The result always shows 0 sec. for any sized PDB file. For example, it takes
about 10 sec. for 1L7A.pdb (by my watch) which contains about 5000 atoms.
However, if I run the above codes in PyMOL command-line mode, it shows
Elapsed time: 0 sec. 

Currently, I am using PyMOL 1.1b4edu (May 2008) on Windows XP.

Should I use other APIs for checking the performance?



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[PyMOL] question about checking the performance of PyMOL

[Joonghyun Ryu]

Hi, all

I am sending this email for asking you about checking the performance of
PyMOL.
I tried to check the elapsed time for the computation of a molecular surface
as follows.

--
import os
import cmd
import pymol

cmd.set(surface_quality, 2)

start = time.time()
cmd.show(surface)
end = time.time() 
elapsedTime = (end - start)
print Elapsed time: , elapsedTime, sec.

--

The result always shows 0 sec. for any sized PDB file. For example, it takes
about 10 sec. for 1L7A.pdb (by my watch) 
which contains about 5000 atoms. However, if I run the above codes in PyMOL
command-line mode, 
it shows Elapsed time: 0 sec. 

Currently, I am using PyMOL 1.1b4edu (May 2008) on Windows XP.

Should I use other APIs for checking the performance?

Re: [PyMOL] question about checking the performance of PyMOL

[DeLano Scientific]

 
Joonghyun,

To optimize performance and responsiveness, PyMOL tends to defer
compute-intensive tasks until their results are actually needed.  Thus,

cmd.show(surface)

Doesn't actually show a surface, it only sets the surface visibility flag on
the atoms present (for future reference).  An actual surface won't be
computed until PyMOL is asked to refresh or render the display.  When
running a script, you can force an update by calling:

cmd.refresh()

After cmd.show.

Cheers,
Warren



--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com


-Original Message-
From: Joonghyun Ryu [mailto:jh...@voronoi.hanyang.ac.kr] 
Sent: Friday, October 24, 2008 10:39 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] question about checking the performance of PyMOL

Hi, all

I am sending this email for asking you about checking the performance of
PyMOL.
I tried to check the elapsed time for the computation of a molecular surface
as follows.

--
import os
import cmd
import pymol

cmd.set(surface_quality, 2)

start = time.time()
cmd.show(surface)
end = time.time()
elapsedTime = (end - start)
print Elapsed time: , elapsedTime, sec.

--

The result always shows 0 sec. for any sized PDB file. For example, it takes
about 10 sec. for 1L7A.pdb (by my watch) which contains about 5000 atoms.
However, if I run the above codes in PyMOL command-line mode, it shows
Elapsed time: 0 sec. 

Currently, I am using PyMOL 1.1b4edu (May 2008) on Windows XP.

Should I use other APIs for checking the performance?



-
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Re: [PyMOL] question on making movie between two scenes with differentpoint of view

[DeLano Scientific]

Junjun,

What version are you using?

Your script should work out of the box with the very latest PyMOL builds and
open-source code.

Prior to release 1.1, movies and scenes didn't work together so well because
of timing issues (use of wall clock versus frame/movie clock).  Those issues
are finally behind us.

The only change I would suggest would be to allow at least 90 frames (3
seconds) between scenes so that the camera interpolation has time to
complete.

Cheers,
Warren

--
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Subscriber Support Services
mailto:supp...@delsci.com


-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of liu junjun
Sent: Monday, June 23, 2008 9:55 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] question on making movie between two scenes with
differentpoint of view

Hello everybody,

I'm trying to make a movie for chaning the point of view on a structure. I
let PyMol read in matrix then define it as a scene. After the movie was set
up, I can watch the movie playing well on the PyMol window. However, if I
try to save the PNG sequence, I get few discontinuous picutures and a lot of
identical pictures. Can anybody please give me some suggestions? Thanks in
advance!

Please see the following script that I wrote for making the movie.

 script for make movie 
# read in point of view for two scene
@pml/view-ts3ab.pml
scene int3b , store
@pml/view-ts4.pml
scene int3b2 , store

# set up a movie
mset 1 x100
mdo 1: scene int3b
mdo 50: scene int3b2
mplay

# save the PNG sequences
set ray_trace_frames = 1
set cache_frame = 0
mpng png/int3b

===

All the best!

Junjun

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Re: [PyMOL] Question about PyMOL development

[DeLano Scientific]

Fengyuan,
 
Unfortunately, the PyMOL's internal gui pop-up menu system was not designed
as nor intended to be a programmers interface and is subject to change at
any time.  Any code which relies upon its behavior may therefore break with
future versions of the software.  
 
 
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com

  _  

From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of NeO
Sent: Sunday, June 22, 2008 7:46 AM
To: supp...@delsci.com; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Question about PyMOL development


Hi Warren,

I've read 'Executive.c' under '/trunk/pymol/layer3', it seems that you've
pre-defined all the cases that button actions and popup menu changes in
function ' ExecutiveClick ', I can understand only part of it. Now, I'm
wondering that if I want to implement my thought ( - left-click the C-alpha
atom in the structure, there will be a PopUp window coming out with
self-defined information in the Viewer window), I have to modify the source
code in C-layer and compile the whole source? Am I right? Or, is there any
trick to do this in Python-layer? 

Fengyuan


On Sun, Jun 22, 2008 at 1:59 PM, NeO bobop...@gmail.com wrote:


Dear Warren,

How are you?


I'm writing a wizard, in which I want to implement the function that when I
left-click the C-alpha atom, there will be a PopUp window coming out with my
defined information in the Viewer window. I can do it using
'tkMessageBox.showinfo', but I want to make it beautiful.

I know that when you left-double click or right-click the protein structure,
the popup menu show up. I read the source code of 'menu.py', I'm not sure in
the function, the parameter 'self_cmd', what's it for? where the menu
functions are called? If I figure it out, I think I can code it in my
wizard.

Hope you can help me :)

Best Wishes

Fengyuan

Re: [PyMOL] Question about PyMOL development

[DeLano Scientific]

Fengyuan,
 
Although we cannot answer specific questions about an unsupported interface,
your question about self_cmd is relevant to the overall project since we
are intending to support multiple PyMOL instances within a single Python
interpreter via: 
 
from pymol2 import PyMOL
 
instance1 = PyMOL()
instance2 = PyMOL()
 
Thus, the old way of messaging the PyMOL API:
 
from pymol import cmd
 
will not work correctly if there two or more active instances.  Instead,
each instance has its own cmd module and programming interface:
 
instance1.cmd
 
instance2.cmd
 
For example:
 
instance1.cmd.load(pdb1.pdb)
 
instance2.cmd.load(pdb2.pdb)
 
As for self_cmd, all Python-based code called from the C layer must
therefore be given a handle pointing at the instance from which it was
called so that it can do useful work. This is the role of the self_cmd
argument, and you'll see similar constructs in both the Python-based wizards
and the Tcl/Tk GUIs.
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com

  _  

From: DeLano Scientific [mailto:del...@delsci.info] 
Sent: Monday, June 23, 2008 9:31 AM
To: 'NeO'; 'supp...@delsci.com'; 'pymol-users@lists.sourceforge.net'
Subject: RE: [PyMOL] Question about PyMOL development


Fengyuan,
 
Unfortunately, the PyMOL's internal gui pop-up menu system was not designed
as nor intended to be a programmers interface and is subject to change at
any time.  Any code which relies upon its behavior may therefore break with
future versions of the software.  
 
 
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com

  _  

From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of NeO
Sent: Sunday, June 22, 2008 7:46 AM
To: supp...@delsci.com; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Question about PyMOL development


Hi Warren,

I've read 'Executive.c' under '/trunk/pymol/layer3', it seems that you've
pre-defined all the cases that button actions and popup menu changes in
function ' ExecutiveClick ', I can understand only part of it. Now, I'm
wondering that if I want to implement my thought ( - left-click the C-alpha
atom in the structure, there will be a PopUp window coming out with
self-defined information in the Viewer window), I have to modify the source
code in C-layer and compile the whole source? Am I right? Or, is there any
trick to do this in Python-layer? 

Fengyuan


On Sun, Jun 22, 2008 at 1:59 PM, NeO bobop...@gmail.com wrote:


Dear Warren,

How are you?


I'm writing a wizard, in which I want to implement the function that when I
left-click the C-alpha atom, there will be a PopUp window coming out with my
defined information in the Viewer window. I can do it using
'tkMessageBox.showinfo', but I want to make it beautiful.

I know that when you left-double click or right-click the protein structure,
the popup menu show up. I read the source code of 'menu.py', I'm not sure in
the function, the parameter 'self_cmd', what's it for? where the menu
functions are called? If I figure it out, I think I can code it in my
wizard.

Hope you can help me :)

Best Wishes

Fengyuan

[PyMOL] question on making movie between two scenes with different point of view

[liu junjun]

Hello everybody,

I'm trying to make a movie for chaning the point of view on a
structure. I let PyMol read in matrix then define it as a scene. After
the movie was set up, I can watch the movie playing well on the PyMol
window. However, if I try to save the PNG sequence, I get few
discontinuous picutures and a lot of identical pictures. Can anybody
please give me some suggestions? Thanks in advance!

Please see the following script that I wrote for making the movie.

 script for make movie 
# read in point of view for two scene
@pml/view-ts3ab.pml
scene int3b , store
@pml/view-ts4.pml
scene int3b2 , store

# set up a movie
mset 1 x100
mdo 1: scene int3b
mdo 50: scene int3b2
mplay

# save the PNG sequences
set ray_trace_frames = 1
set cache_frame = 0
mpng png/int3b

===

All the best!

Junjun

Re: [PyMOL] Question about PyMOL development

[NeO]

Dear Warren,

How are you?

I'm writing a wizard, in which I want to implement the function that when I
left-click the C-alpha atom, there will be a PopUp window coming out with my
defined information in the Viewer window. I can do it using
'tkMessageBox.showinfo', but I want to make it beautiful.

I know that when you left-double click or right-click the protein structure,
the popup menu show up. I read the source code of 'menu.py', I'm not sure in
the function, the parameter 'self_cmd', what's it for? where the menu
functions are called? If I figure it out, I think I can code it in my
wizard.

Hope you can help me :)

Best Wishes

Fengyuan

Re: [PyMOL] Question about PyMOL development

[NeO]

Hi Warren,

I've read 'Executive.c' under '/trunk/pymol/layer3', it seems that you've
pre-defined all the cases that button actions and popup menu changes in
function ' ExecutiveClick ', I can understand only part of it. Now, I'm
wondering that if I want to implement my thought ( - left-click the C-alpha
atom in the structure, there will be a PopUp window coming out with
self-defined information in the Viewer window), I have to modify the source
code in C-layer and compile the whole source? Am I right? Or, is there any
trick to do this in Python-layer?

Fengyuan

On Sun, Jun 22, 2008 at 1:59 PM, NeO bobop...@gmail.com wrote:

 Dear Warren,

 How are you?

 I'm writing a wizard, in which I want to implement the function that when I
 left-click the C-alpha atom, there will be a PopUp window coming out with my
 defined information in the Viewer window. I can do it using
 'tkMessageBox.showinfo', but I want to make it beautiful.

 I know that when you left-double click or right-click the protein
 structure, the popup menu show up. I read the source code of 'menu.py', I'm
 not sure in the function, the parameter 'self_cmd', what's it for? where the
 menu functions are called? If I figure it out, I think I can code it in my
 wizard.

 Hope you can help me :)

 Best Wishes

 Fengyuan

[PyMOL] question about SUPER

[Jianghai Zhu]

Hi,

I am using SUPER to superimpose different structures in PyMOL.  And I  
noticed that when I try to superimpose a lot of different structures  
onto one reference structure, the number of aligned atoms is getting  
smaller and smaller as I keep using SUPER command.  And eventually  
structures cannot be aligned anymore even though the first few  
structures are aligned quite well.  So is this a bug?


Jianghai


Jianghai Zhu, PhD
Immune Disease Institute
Dept. of Pathology
Harvard Medical School
200 Longwood Ave.
Boston, MA 02115
Tel: 617-278-3211
Fax: 617-278-3232

Re: [PyMOL] question about SUPER

[DeLano Scientific]

Jianghai,

That sounds like a bug, but it could be something specific about your
script.  Could you post (or email us) an example PyMOL script which
reproduces the reported behavior?

Thanks!
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com


-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Jianghai Zhu
Sent: Thursday, June 05, 2008 8:26 AM
To: pymol-users
Subject: [PyMOL] question about SUPER

Hi,

I am using SUPER to superimpose different structures in PyMOL.  And I
noticed that when I try to superimpose a lot of different structures onto
one reference structure, the number of aligned atoms is getting smaller and
smaller as I keep using SUPER command.  And eventually structures cannot be
aligned anymore even though the first few structures are aligned quite well.
So is this a bug?

Jianghai


Jianghai Zhu, PhD
Immune Disease Institute
Dept. of Pathology
Harvard Medical School
200 Longwood Ave.
Boston, MA 02115
Tel: 617-278-3211
Fax: 617-278-3232







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[PyMOL] FW: Pymol question

[DeLano Scientific]

 
 I have a quick question for you.
 I am trying to look at the structure of the tetranucleosome (pdb file
1zbb).
 However, the structure is only composed by 2 nucleosomes. Is there a way
to duplicate the image to 4?

Based on the BIOMT records in the PDB file:

REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, J, A, B, C, D, E, F, G,
REMARK 350 H, a, b, c, d, e, f, g, h
REMARK 350   BIOMT1   1  1.00  0.00  0.000.0
REMARK 350   BIOMT2   1  0.00  1.00  0.000.0
REMARK 350   BIOMT3   1  0.00  0.00  1.000.0
REMARK 350   BIOMT1   2 -1.00  0.00  0.00  127.67500
REMARK 350   BIOMT2   2  0.00  1.00  0.000.0
REMARK 350   BIOMT3   2  0.00  0.00 -1.00  237.12600

You can create the biological unit as follows:

# load the PDB file

fetch 1zbb, async=0

# create a copy

create 1zbb_2, 1zbb

# transform the copy according to the second matrix above

alter_state 1, 1zbb_2, (x,y,z)=(127.675-x, y, 237.126-z)

Cheers,
Warren

[PyMOL] Question about electron density map with mtz file

[adi di]

Dear all,

I am trying to put on the electron density. I only
have .mtz file but I have a look at the manual and the
program need XPLOR file. How can I get the XPLOR file
or do I need to convert the mtz file to this - if so
how can I do that? Thank you very much

Best Regards
Adiphol


   
Be
 a better Globetrotter. Get better travel answers from someone who knows. 
Yahoo! Answers - Check it out.
http://answers.yahoo.com/dir/?link=listsid=396545469

Re: [PyMOL] Question about electron density map with mtz file

[Robert Campbell]

Hi Adiphol

* adi di adipho...@yahoo.com [2007-05-11 10:26] wrote:
 Dear all,
 
 I am trying to put on the electron density. I only
 have .mtz file but I have a look at the manual and the
 program need XPLOR file. How can I get the XPLOR file
 or do I need to convert the mtz file to this - if so
 how can I do that? Thank you very much

Actually PyMOL can read ccp4 format maps, but they have to be maps, not
the mtz reflection file with the columns h, k, l, FWT, PHWT etc. as
output by refmac and other programs.  If you ask refmac to output a CCP4
format map, then PyMOL can read it:

load filename.map, map_obj, format=ccp4

will load the map and create an object called map_obj.  The latter then
needs to be contoured by PyMOL.  For example:

  isomesh lev1, map_obj, selection=molecule  c. a   resi 100, level=1, 
buffer=8.

would create an object called lev1 with a contour level of 1 in a box of
8Angstroms around residue 100 of chain a of molecule.

Hope that helps,

Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] question on state

[Tsjerk Wassenaar]

Hi David,

The state sort of refers to the frame or model in case of a
multiframe/multimodel (multistate) system. You don't need to use it
with set, it's optional. Just note that dash_length and dash_length
are quite different things.

Best,

Tsjerk

On 3/28/07, David Shin dav...@scripps.edu wrote:

This regards to my last post.

I finally got it with:
PyMOLset dash_length, 0.1, measure01, 1

and got the message:
Setting: dash_length set to 0.1 in object measure01, state 1.

but was wondering what state actually refers too...

ie. previously, I tried:
PyMOLset dash_length, 0.1, measure01

and got the error:
Error: unknown setting 'dash_length'.

which is why asked the question before.

Thanks,
Dave

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Re: [PyMOL] question on state

[DeLano Scientific]

Will,

The easiest approach, short of Python programming, is to temporarily load a
new pdb file with updated coordinates and simply update the existing object
before deleting the original.

load original.pdb
unset auto_zoom

# then repeat the following as often as necessary

set suspend_updates
load updated.pdb
update original,updated
delete updated
unset suspend_updates

Cheers,
Warren

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Subscriber Support Services
mailto:del...@delsci.info


I'm interested prototyping some interactive molecular modeling and
simulation code using pymol. I know one can change the atomic coordinates
wholesale in simple ways via alter_state (like x=x+1). Is there an efficient
way to change all coordinates to arbitrary values (like coordinates output
from a simulation)? I could select each atom and alter_state it's xyz
values, but I'm hoping there is a better way. 

Thanks!

-Will Sheffler
Baker Lab
University of Washington

[PyMOL] question on state

[David Shin]

This regards to my last post.

I finally got it with:
PyMOLset dash_length, 0.1, measure01, 1

and got the message:
Setting: dash_length set to 0.1 in object measure01, state 1.

but was wondering what state actually refers too...

ie. previously, I tried:
PyMOLset dash_length, 0.1, measure01

and got the error:
Error: unknown setting 'dash_length'.

which is why asked the question before.

Thanks,
Dave

Re: [PyMOL] PyMol question?

[Tsjerk Wassenaar]

Hi,

You can do this using alter_state:

alter_state 1,selection,(x,y,z) =
  (a11*x+a12*y+a13*z+d1, a21*x+a22*y+a23*z+d2,
a31*x+a32*y+a33*z+d3)

where a11-a33 are the matrix elements (check whether they have to be
transposed) and d1-d3 are the elements of the shift vector.

It may be convenient to make this a function which you can load at
startup time (especially if you have to do this many times). For
example, paste the following in a file mtransform.py:

from pymol import cmd

def mtransform( selection=all, matrix=[[1,0,0],[0,1,0],[0,0,1],[0,0,0]] ):
   if ( len(matrix) == 3 ): # In this way it is also valid to give a
3x3 matrix for rotation only
   matrix.append( [0,0,0] )
   a11, a12, a13 = matrix[0][0], matrix[0][1], matrix[0][2]
   a21, a22, a23 = matrix[1][0], matrix[1][1], matrix[1][2]
   a31, a32, a33 = matrix[2][0], matrix[2][1], matrix[2][2]
   d1,  d2,  d3  = matrix[0][0], matrix[0][1], matrix[0][2]
   cmd.alter_state( 1, selection, (x,y,z) = (%f*x+%f*y+%f*z+%f,
%f*x+%f*y+%f*z+%f, %f*x+%f*y+%f*z+%f ) %
(a11,a12,a13,d1,a21,a22,a23,d2,a31,a32,a33,d3)

#

Of course it could be done more efficiently, better looking, but that
is left as an exercise for the reader ;) (Think of changing
coordinates directly, adding an option to make a copy of the selection
first, and parse a string for the matrix, such that you can use
cmd.extend and can run the command using:

mtransform all, [[0,1,0],[-1,0,0],[0,0,1],[3,1,2]]

rather than:

mtransform(all, [[0,1,0],[-1,0,0],[0,0,1],[3,1,2]])

which is the way to invoke the command with the given code.

Hope this helps,

Tsjerk

On 6/30/06, Peter Adrian Meyer pa...@cornell.edu wrote:

The easiest way I'm aware of to do this would be to use the ccp4 program
pdbset, but there are numerous other ways/programs that will do this (if
pymol has this capacity, I'm not aware of it; but someone else will
correct me).

Pete

snip

 I've been looking through the PyMol reference and wiki page and I can't
find a command for moving a molecule through a matrix, I
 would like to move one pdb onto the other using the info below. Is
there such a command?
 ## MATRICES: UX+T is the least-squares superimposition of STRID2 (X)
onto STRID1
   NR. STRID1 STRID2   U(.,1)U(.,2)U(.,
 3) T(.)
1: 9506-A 1risU(1,.)  -0.230692 -0.010007
 -0.972975   50.701385
1: 9506-A 1risU(2,.)   0.443459  0.888979
 -0.114287   31.716473
1: 9506-A 1risU(3,.)   0.866098 -0.457839
 -0.200643   26.479412



Pete Meyer
Fu Lab
BMCB grad student
Cornell University





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Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Re: [PyMOL] PyMol question?

[William Scott]

Hi Mark:

Most likely there is, but I don't know the answer to your question.  
I'm posting this to the pymol users list (via cc) so hopefully  
someone else will know the answer.


I trust all is going well for you.

Bill


On Jun 30, 2006, at 8:19 AM, Mark Collins wrote:


Hi Bill,

I've been looking through the PyMol reference and wiki page and I  
can't find a command for moving a molecule through a matrix, I  
would like to move one pdb onto the other using the info below. Is  
there such a command?


## MATRICES: UX+T is the least-squares superimposition of STRID2  
(X) onto STRID1
  NR. STRID1 STRID2   U(.,1)U(.,2)U(., 
3) T(.)
   1: 9506-A 1risU(1,.)  -0.230692 -0.010007  
-0.972975   50.701385
   1: 9506-A 1risU(2,.)   0.443459  0.888979  
-0.114287   31.716473
   1: 9506-A 1risU(3,.)   0.866098 -0.457839  
-0.200643   26.479412


Thanks Mark

Re: [PyMOL] PyMol question?

[Peter Adrian Meyer]

The easiest way I'm aware of to do this would be to use the ccp4 program
pdbset, but there are numerous other ways/programs that will do this (if
pymol has this capacity, I'm not aware of it; but someone else will
correct me).

Pete

snip

 I've been looking through the PyMol reference and wiki page and I can't
find a command for moving a molecule through a matrix, I
 would like to move one pdb onto the other using the info below. Is
there such a command?
 ## MATRICES: UX+T is the least-squares superimposition of STRID2 (X)
onto STRID1
   NR. STRID1 STRID2   U(.,1)U(.,2)U(.,
 3) T(.)
1: 9506-A 1risU(1,.)  -0.230692 -0.010007
 -0.972975   50.701385
1: 9506-A 1risU(2,.)   0.443459  0.888979
 -0.114287   31.716473
1: 9506-A 1risU(3,.)   0.866098 -0.457839
 -0.200643   26.479412



Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Re: [PyMOL] Question on rotation

[Tsjerk Wassenaar]

Hi Terry,

There's a bit more to it. In the pymol view, the camera is located at the
origin, so to rotate your coordinates you first have to move the center to
the origin, do the rotation and move the thing back. I've scripted this in
Povray. If you're interested, I can send you the script. You can then
rescript it in python or you can output your scene to povray and do the rest
there.

In addition (although you may already know this), the meaning of all
elements of the result of get_view (python index) is

0:9 - rotation matrix
9:12 - camera position
12:15 - origin of rotation
15:17 - slab near and far
17 - orthoscopic flag

Cheers,

Tsjerk


On 4/25/06, Terry Jones tc...@cam.ac.uk wrote:

 I wrote a pymol plugin that produces a bunch of cgo. The images I generate
 have a cube drawn around them.

 I've been asked if it's possible to allow the user to initially rotate the
 image to their heart's content and then have the plugin draw the
 surrounding cube. I.e., once the image is rotated, the cube will be drawn
 in a way that always looks good to the viewer, not at some random angle.
 In
 other words, the cube will always have the same orientation, no matter how
 much the image has been rotated before the cube is drawn.

 OK, having said the same thing 3 times, and hopefully made sense at least
 once, I'll say something new...

 I imagine this can be done easily enough. I guess I should be able to call
 get_view and get the current rotation matrix (elements 0-8 of the returned
 list) and apply this to all points that I plan to draw between when making
 the cube.

 My questions: Is this right? Do I need to do anything more than just
 multiply the old point by the rotation matrix? What's the easiest way to
 do
 this in Pymol or Python, or should I just code it (it's very simple after
 all).  And, of course, is there a better way to do what I want?

 Thanks for any help. Don't assume I know what I'm doing, because I
 probably
 don't. So the more details, the better.

 Regards,
 Terry


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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Re: [PyMOL] Question on rotation

[Terry Jones]

Hi Tsjerk

 Tsjerk == Tsjerk Wassenaar tsje...@gmail.com writes:
Tsjerk There's a bit more to it. In the pymol view, the camera is located
Tsjerk at the origin, so to rotate your coordinates you first have to move
Tsjerk the center to the origin, do the rotation and move the thing
Tsjerk back. I've scripted this in Povray. If you're interested, I can
Tsjerk send you the script.

Yes, that sounds great, thanks.

Tsjerk You can then rescript it in python or you can
Tsjerk output your scene to povray and do the rest there.

If it's not too complex, I'll rewrite for python so I can run it
interactively.

Tsjerk In addition (although you may already know this), the meaning of
Tsjerk all elements of the result of get_view (python index) is

Yes, thanks a lot.

Terry

[PyMOL] Question on rotation

[Terry Jones]

I wrote a pymol plugin that produces a bunch of cgo. The images I generate
have a cube drawn around them.

I've been asked if it's possible to allow the user to initially rotate the
image to their heart's content and then have the plugin draw the
surrounding cube. I.e., once the image is rotated, the cube will be drawn
in a way that always looks good to the viewer, not at some random angle. In
other words, the cube will always have the same orientation, no matter how
much the image has been rotated before the cube is drawn.

OK, having said the same thing 3 times, and hopefully made sense at least
once, I'll say something new...

I imagine this can be done easily enough. I guess I should be able to call
get_view and get the current rotation matrix (elements 0-8 of the returned
list) and apply this to all points that I plan to draw between when making
the cube.

My questions: Is this right? Do I need to do anything more than just
multiply the old point by the rotation matrix? What's the easiest way to do
this in Pymol or Python, or should I just code it (it's very simple after
all).  And, of course, is there a better way to do what I want?

Thanks for any help. Don't assume I know what I'm doing, because I probably
don't. So the more details, the better.

Regards,
Terry

Re: [PyMOL] Question about how to replace the amino acid

[Noinaj]

Adi,

I have forwarded you some previous discussions on mutations.  You will find 
your answer below.  If you need anything further, please let me know.


Best of Luck!


Cheers,
Nick

---
Hi,

I would like to ask how to change (modify or replace)
the amino acid residue? I'm using MacPymol and my
computer is iBookG4.

Thank you very much
Adi



- Original Message - 
From: Andrew Colasanti acolasa...@gmail.com

To: pymol-users@lists.sourceforge.net
Sent: Thursday, April 20, 2006 9:36 AM
Subject: Re: [PyMOL] mutations


I follow the method outlined by Nick with one additional step, after
selecting the new residue you can run through a sidechain rotamer
library using the forward arrows at the bottom of the window.  You
also have a choice to use backbone dependant or backbone independant
rotamers.

Andrew

On 4/18/06, Noinaj noi...@uky.edu wrote:


Orla,

This is simply, for the most part.  Here is what I do.

Load your *.pdb file.  Then under WIZARD in the menu bar, select
MUTAGENESIS.  Then pretty much, follow directions.  In the PyMOL VIEWER
window, it will ask you to ' pick a residue.'  Once you pick a residue,
select the type of residue you want to mutate to by left clicking on [No
Mutation] button and holding down (under Mutagenesis).  This brings up a
list of residues that you can then select from.  Once you select the 
residue

you want, hit APPLY, then DONE.  If everything was done correctly, you
should see your mutated residue.

There are probably other ways to do this, but I hope this helps.  If you
would like screenshots of the steps, just let me know.



Cheers,
Nick




- Original Message -
From: Orla O'Sullivan
To: pymol-users@lists.sourceforge.net
Sent: Tuesday, April 18, 2006 11:31 AM
Subject: [PyMOL] mutations




Hi all

I'm a newbie to Pymol and so far have been very impressed. However I have
tried to mutate some residues in my structure and have hit a brick wall.

Has anyone done this with pymol and let me know how to do it?



Regards



Orla



Dr.Orla O'Sullivan

Research Officer

Biotechnology





Moorepark Food Research Centre
Teagasc

Moorepark
Fermoy, Co. Cork
Ireland




Tel:   +353 - (0)25 - 42344





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[PyMOL] Question about how to replace the amino acid

[adi di]

Hi,

I would like to ask how to change (modify or replace)
the amino acid residue? I'm using MacPymol and my
computer is iBookG4. 

Thank you very much 
Adi 

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Re: [PyMOL] question about ca trace

[Tsjerk Wassenaar]

Hi Tiger,

Nick is largely right. The cause for the link to show up is that pymol just
traces through all c-alphas in the object, regardless of chains or
distances. So, selecting the linked residues and hiding the trace should
solve your problem. Also, creating two files will do the trick.
Alternatively, you can create two objects and draw the trace for each of
these.

Cheers,

Tsjerk

On 4/13/06, Noinaj noi...@uky.edu wrote:

 Tiger,

 I am no expert by far, but can you select the linkage?  If so, just select
 and hide.  Also, you might try just hiding the two residues that are
 linked,
 this might get rid of the link and you probably wouldn't notice the
 missing
 residues unless it is a small protein.  alternatively, and probably the
 best
 solution is to edit the pdb file to create two individual files, one for
 each dimer (this can be done in any text editor).  then open both in Pymol
 and you should then be able to edit independently.

 The problem may be, and again I remind you that I am no expert, that these
 atoms are two close to each other and may be getting mistaken for a
 covalent
 interaction, can't tell without actually seeing though.

 Hope any or all of this helps.  Good Luck!



 Cheers,
 Nick






 - Original Message -
 From: Geng Tian gengt...@hotmail.com
 To: pymol-users@lists.sourceforge.net
 Sent: Thursday, April 13, 2006 3:19 PM
 Subject: [PyMOL] question about ca trace


  Hi, There:
  I have a pdb file for a dimer. only coordinates of alph carbons are in
 the
  pdb. In the pymol, I
  set cartoon_trace, 1
  and
  show cartoon
  each monomer is fine but a weird linkage showed up between the last
  residue of chain a and first residue of chain b. I just can't remove
 this
  ugly linkage. Do you have any idea? Thank you. Actually I tried ribbon
  mode and no this weird linkage but I like the figure qualify of the
  cartoon.
  Tiger
 
  _
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Re: [PyMOL] question about ca trace

[Noinaj]

Tsjerk,

Nice point, and probably easier to just create new objects in Pymol.  



nick


  - Original Message - 
  From: Tsjerk Wassenaar 
  To: pymol-users@lists.sourceforge.net 
  Sent: Friday, April 14, 2006 4:29 AM
  Subject: Re: [PyMOL] question about ca trace


  Hi Tiger,

  Nick is largely right. The cause for the link to show up is that pymol just 
traces through all c-alphas in the object, regardless of chains or distances. 
So, selecting the linked residues and hiding the trace should solve your 
problem. Also, creating two files will do the trick. Alternatively, you can 
create two objects and draw the trace for each of these.

  Cheers,

  Tsjerk


  On 4/13/06, Noinaj noi...@uky.edu wrote:
Tiger,

I am no expert by far, but can you select the linkage?  If so, just select
and hide.  Also, you might try just hiding the two residues that are linked,
this might get rid of the link and you probably wouldn't notice the missing 
residues unless it is a small protein.  alternatively, and probably the best
solution is to edit the pdb file to create two individual files, one for
each dimer (this can be done in any text editor).  then open both in Pymol 
and you should then be able to edit independently.

The problem may be, and again I remind you that I am no expert, that these
atoms are two close to each other and may be getting mistaken for a covalent
interaction, can't tell without actually seeing though. 

Hope any or all of this helps.  Good Luck!



Cheers,
Nick






- Original Message -
From: Geng Tian gengt...@hotmail.com 
To: pymol-users@lists.sourceforge.net
Sent: Thursday, April 13, 2006 3:19 PM
Subject: [PyMOL] question about ca trace


 Hi, There: 
 I have a pdb file for a dimer. only coordinates of alph carbons are in the
 pdb. In the pymol, I
 set cartoon_trace, 1
 and
 show cartoon
 each monomer is fine but a weird linkage showed up between the last 
 residue of chain a and first residue of chain b. I just can't remove this
 ugly linkage. Do you have any idea? Thank you. Actually I tried ribbon
 mode and no this weird linkage but I like the figure qualify of the 
 cartoon.
 Tiger

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  -- 

  Tsjerk A. Wassenaar, M.Sc.
  Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
  Dept. of Biophysical Chemistry
  University of Groningen
  Nijenborgh 4
  9747AG Groningen, The Netherlands
  +31 50 363 4336

Re: [PyMOL] question about ca trace

[Noinaj]

Tiger,

I am no expert by far, but can you select the linkage?  If so, just select 
and hide.  Also, you might try just hiding the two residues that are linked, 
this might get rid of the link and you probably wouldn't notice the missing 
residues unless it is a small protein.  alternatively, and probably the best 
solution is to edit the pdb file to create two individual files, one for 
each dimer (this can be done in any text editor).  then open both in Pymol 
and you should then be able to edit independently.


The problem may be, and again I remind you that I am no expert, that these 
atoms are two close to each other and may be getting mistaken for a covalent 
interaction, can't tell without actually seeing though.


Hope any or all of this helps.  Good Luck!



Cheers,
Nick






- Original Message - 
From: Geng Tian gengt...@hotmail.com

To: pymol-users@lists.sourceforge.net
Sent: Thursday, April 13, 2006 3:19 PM
Subject: [PyMOL] question about ca trace



Hi, There:
I have a pdb file for a dimer. only coordinates of alph carbons are in the 
pdb. In the pymol, I

set cartoon_trace, 1
and
show cartoon
each monomer is fine but a weird linkage showed up between the last 
residue of chain a and first residue of chain b. I just can't remove this 
ugly linkage. Do you have any idea? Thank you. Actually I tried ribbon 
mode and no this weird linkage but I like the figure qualify of the 
cartoon.

Tiger

_
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http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/




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[PyMOL] Question about surface property calculations

[Benjamin Hitz]

Hello all -

As a grad student, I used Grasp to do extensive (albeit) simple  
calculations on surface properties.
Grasp specifically assigned floats or ints to specific surface  
vertices (triangles) which could be assigned to subsets and  
calculated upon.


I am interested in possibly doing similar work with PyMol.  I might  
want to, for example, calculate the average of a specifically  
assigned numerical property over an interface and write it to a  
file.I would also like to calculate a local surface  
curvature (something like what grasp does with the green/grey  
coloring scheme), I would guess that this is not currently possibly  
in PyMol.


Would I have to write a plugin for PyMol to do this kind of stuff?  I  
am guessing that the numerically intense stuff would have to be done  
in C/C++.


Thanks for you time,

Ben


--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium

Stanford University ** h...@genome.stanford.edu

Re: [PyMOL] Question about custom CGO objects

[Gilleain Torrance]

Hi,

As I understand it, you can either make cgo's that are 'static' in  
shape (like a 3D stamp) or use pymol.callback objects, which can use  
arbitrary opengl commands (such as matrix rotations).


I actually made a cone, in response to someone's query, only I had to  
use callbacks to get triangle fans, and it appears that macpymol  
doesn't have opengl compiled in by default or something.


Here is my Cone class (mostly nicked from a tutorial on the web):

import math
from pymol.opengl.gl import *
from pymol.callback import Callback
from pymol import cmd

class Cone(Callback):

def get_extent(self):
return [[-10.0, -10.0, -10.0], [10.0, 10.0, 10.0]]

def __call__(self):
glPushMatrix()
glRotatef(xRot, 1.0, 0.0, 0.0)
glRotatef(yRot, 0.0, 1.0, 0.0)

# Begin a triangle fan
glBegin(GL_TRIANGLE_FAN)

# Pinnacle of cone is shared vertex for fan, moved up z-axis
# to produce a cone instead of a circle
glVertex3f(0.0, 0.0, 75.0)

# Loop around in a circle and specify even points along the  
circle

# as the vertices of the triangle fan
angle = 0.0
while angle  2.0 * math.pi:

# Calculate x and y position of the next vertex
x = 50.0 * math.sin(angle)
y = 50.0 * math.cos(angle)

# Alternate color between red and green
if((iPivot %2) == 0):
glColor3f(0.0, 1.0, 0.0)
else:
glColor3f(1.0, 0.0, 0.0)

# Increment pivot to change color next time
iPivot += 1

# Specify the next vertex for the triangle fan
glVertex2f(x, y)
angle += (math.pi / 8.0)

# Done drawing fan for cone
glEnd()

# Begin a new triangle fan to cover the bottom
glBegin(GL_TRIANGLE_FAN)

# Center of fan is at the origin
glVertex2f(0.0, 0.0)
angle = 0.0
while angle  2.0 * math.pi:
# Calculate x and y position of the next vertex
x = 50.0 * math.sin(angle)
y = 50.0 * math.cos(angle)

# Alternate color between red and green
if((iPivot %2) == 0):
glColor3f(0.0, 1.0, 0.0)
else:
glColor3f(1.0, 0.0, 0.0)

# Increment pivot to change color next time
iPivot += 1

# Specify the next vertex for the triangle fan
glVertex2f(x, y)
angle += (math.pi / 8.0)

# Done drawing the fan that covers the bottom
glEnd()

# Restore transformations
glPopMatrix()


rx, ry, rz = 1, 2, 3
cmd.load_callback(Cone(), 'cone')


Gilleain Torrance

On 8 Nov 2005, at 06:44, Andrew Wollacott wrote:


Hey all,
I recently made a cone class that will display cones using pymol
cgo's.  I built the cones using triangles as suggested by Warren  Now
I need to get the cones oriented properly, so I was wondering if it's
possible to apply a GL or rotation matrix when making the cgo.  I
guess if I can't do this then I can rotate the vertices of each
individual triangle, but I only want to do this as a last resort.

Any help would be appreciated.

Thanks,

Andrew Wollacott, PhD
Baker Research Group
The University of Washington


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[PyMOL] Question about custom CGO objects

[Andrew Wollacott]

Hey all,
I recently made a cone class that will display cones using pymol
cgo's.  I built the cones using triangles as suggested by Warren  Now
I need to get the cones oriented properly, so I was wondering if it's
possible to apply a GL or rotation matrix when making the cgo.  I
guess if I can't do this then I can rotate the vertices of each
individual triangle, but I only want to do this as a last resort.

Any help would be appreciated.

Thanks,

Andrew Wollacott, PhD
Baker Research Group
The University of Washington

Re: [PyMOL] question about ray after alter and rebuild

[Kristian Rother]

--- Chung-Ming Yu yucm...@gate.sinica.edu.tw wrote:

 Dear all:
 
 I changed the topology of secondary structures with
 'alter' commands and then
 I used 'rebuild' command to show the new topology of
 secondary structures in
 multiple structura alignment. I pointed out three
 structures for further
 processing within all 12 structures. However, when I
 try to ray the structural
 resolution (only 3 of all 12 structures) to
 2000x2000 with 'ray 2000, 2000', I
 always received a low resolution (as screen
 resolution only) result. How could
 I do? Thanks a lot!
 
 Fisher C.-M. Yu
 
 yucm...@gate.sinica.edu.tw
 
 
 

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Re: [PyMOL] question about ray after alter and rebuild

[Peter Adrian Meyer]

 multiple structura alignment. I pointed out three structures for further
 processing within all 12 structures. However, when I try to ray the
 structural
 resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000,
 2000', I
 always received a low resolution (as screen resolution only) result. How
 could
 I do? Thanks a lot!


Pymol can't display a ray-traced image to higher resolution than your
screen can show, but it can write it to a png file at that resolution (I'm
assuming you're talking about pixel resolution, not diffraction resolution
here).

ray 2000,2000 ; png HighRes.png

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Re: [PyMOL] question about ray after alter and rebuild

[Sabuj Pattanayek]

Or you can dump to povray and render at whatever resolution you want,
but the image will not resemble exactly what is seen in the pymol viewer
window.

Peter Adrian Meyer wrote:
multiple structura alignment. I pointed out three structures for further
processing within all 12 structures. However, when I try to ray the
structural
resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000,
2000', I
always received a low resolution (as screen resolution only) result. How
could
I do? Thanks a lot!
 
 
 
 Pymol can't display a ray-traced image to higher resolution than your
 screen can show, but it can write it to a png file at that resolution (I'm
 assuming you're talking about pixel resolution, not diffraction resolution
 here).
 
 ray 2000,2000 ; png HighRes.png
 
 Pete
 
 Pete Meyer
 Fu Lab
 BMCB grad student
 Cornell University

Re: [PyMOL] question about ray after alter and rebuild

[Peter Adrian Meyer]

 Or you can dump to povray and render at whatever resolution you want,
 but the image will not resemble exactly what is seen in the pymol viewer
 window.


I've noticed problems with the clipping planes (z axis) whenever I've
tried this.  Specifically, the near clipping plane is apparently not
respected in pov-ray conversion (particularly for maps/isomeshes).
I don't know if this has been fixed or not as of yet, but I wasn't able to
find a way to work around this.  Your milage may vary...

Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Re: [PyMOL] question about ray after alter and rebuild

[Tsjerk Wassenaar]

Hi Pete,

Check on the sections clipped_by and bounded_by in the povray
documentation. You can clip with a defined plane, and can actually do so
using different planes for different objects. Alternatively you can use
other objects to clip. Another possibility is to use CSG difference or
intersection. Especially the latter will be painfully slow with surfaces and
such, unfortunately. Come to think of it, it may be possible to directly
include this in the conversion to povray. Maybe if I have a moment, I'll add
it to the scripts I have and post the link... :)

Cheers,

Tsjerk

On 10/24/05, Peter Adrian Meyer pa...@cornell.edu wrote:


  Or you can dump to povray and render at whatever resolution you want,
  but the image will not resemble exactly what is seen in the pymol viewer
  window.
 

 I've noticed problems with the clipping planes (z axis) whenever I've
 tried this. Specifically, the near clipping plane is apparently not
 respected in pov-ray conversion (particularly for maps/isomeshes).
 I don't know if this has been fixed or not as of yet, but I wasn't able to
 find a way to work around this. Your milage may vary...

 Pete


 Pete Meyer
 Fu Lab
 BMCB grad student
 Cornell University



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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

[PyMOL] question about ray after alter and rebuild

[Chung-Ming Yu]

Dear all:

I changed the topology of secondary structures with 'alter' commands and then
I used 'rebuild' command to show the new topology of secondary structures in
multiple structura alignment. I pointed out three structures for further
processing within all 12 structures. However, when I try to ray the structural
resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000, 2000', I
always received a low resolution (as screen resolution only) result. How could
I do? Thanks a lot!

Fisher C.-M. Yu

yucm...@gate.sinica.edu.tw

Re: [PyMOL] question on cctbx and pymol

[Robert Campbell]

Hi,

* Jianghai Zhu z...@purdue.edu [2005-08-24 01:59] wrote:
 
 I could not get cctbx work under either MacPymol or PymolX11Hybrid in 
 Mac OS X.  Anywhere I can find some instructions to get cctbx work in 
 OS X?

There is a page on the cctbx with special instructions for using it on
the Mac:

http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html

Note that you need to use the Framework build of PyMOL:

http://delsci.com/frameworkpymol/

Unfortunately there isn't a Mac around here for me to test this stuff
on.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] question about _cmd.pyd

[wenming hu]

i have written python extend module by c/c++, but i saw a module of pyMOL called
_cmd.pyd instead of _cmd.dll. and it is written by c/c++ also, the author
use makefile to compile it into _cmd.pyd. i have some question about it:
1. what's the difference between them? i saw the code is same as common c++
extended python module, can i use microsoft visual C++ to create a dll
project for compiling it as _cmd.dll?
2. i have never written a module with extension *.pyd, how to make a *.pyd?
and, i doubt, how the author debug the _cmd.pyd, only by Makefile?
3. i have a common problem about writting a extend module by c/c++, i often
use msvc to write it, but i only can invoke release dll, not debug dll, even
i use command like this: python_d test.py, in which case, test.py import
test.dll, and invoke test.hello() api. why? anybody has nice way to debug
it? thank you.

4. how does the author use msvc compile it as cmd.pyd? i did not find any legal 
makefile for msvc6.


any help would be appreciated.


with my best regards,
Wen




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[PyMOL] Re： RE: [PyMOL] question about _cmd.pyd

[wenming hu]

I see. thank you for your answer. and i'm wondering, how do u develop python 
modules like _cmd.pyd? only via setup.py, and type python setup.py build to 
compile it? how do u debug it on the procudure of development? for me, it's not 
easy to develop _cmd.pyd only via setup.py script, i think, there must have 
some other way to debug python extend modules.
 
thank you.
 

Warren DeLano war...@delsci.com

Wen,

The only form of end-user PyMOL compilation we support on Windows is via 
Python's distutils facility. 

Assuming that your system paths are set up correctly, distutils compilations 
will work fine with msvc6 -- no Makefile is required. 

Your own c/c++ code should be built as a standalone DLL -- separate from 
_cmd.*, and you should use the Python interpreter to bring all of the native 
components together at runtime.

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
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